Labeling reagents and methods of their use

ABSTRACT

The present disclosure is directed to a reactive ester agent capable of conjugating a reporter molecule to a carrier molecule or solid support. The reactive ester agent has the general formula: 
                         
wherein the variables are described throughout the application.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Patent Application No.60/887,218 filed Jan. 30, 2007, which disclosure is herein incorporatedby reference.

FIELD OF THE INVENTION

Novel compounds and methods of labeling are disclosed. The dyes areactivated with water solublizing phenolic esters and contacted with acarrier molecule or solid support comprising a nucleophile to yield astable conjugate comprising a dye labeled carrier molecule.

BACKGROUND OF THE INVENTION

The ability to effectively label a target molecule with a dye is highlydependent on the reactive groups present on each of the molecules in thereaction and the conjugation conditions. Reagents such as succinimidylesters (SE) and perfluorophenyl (PFP) esters have high reactivity rateswith water, thereby limiting preparation, packaging, dispensing andpurification conditions and their subsequent shelf life. In addition,due to their hydrolytic reactivity, most of the reagents used forbiomolecule labeling in aqueous buffers hydrolyze prior to reaction withthe desired biomolecule and are therefore wasted.

Gee et al. (Tetrahedron Letters (1999), 40, 1471-1474) describes4-sulfotetrafluorophenyl (STP) esters for use in dye labeling. Thesegroups have been shown to be amenable to conjugation in aqueousenvironments.

Koichi et al. (Chemical & Pharmaceutical Bulletin (1987), 35(3),1044-1048) and Tsuji et al. (Peptide Chemistry (1986), Volume Date 1985,23rd 111-114) describe peptide synthesis via ester activation withpotassium dichlorophenolsulfonate, sodium dibromophenolsulfonate, andsodium nitrophenolsulfonate. No description of labeling or conjugationof molecules such as dyes is provided.

While many labeling reagents exist and have been used with intermittentsuccess, there remains a need for labeling reagents that produce highyields under biologically relevant reaction conditions. Additionally, aneed exists for a conjugation product that is stable and does nothydrolyze in aqueous environments.

SUMMARY OF THE INVENTION

The present invention provides a reactive group, which has much greaterhydrolytic stability than standard N-hydroxysuccinimidyl (SE) andperfluorophenolic (PFP) esters, and when attached to a reporter moleculeforms a labeling reagent of the present invention. Additionally, thelabeling reagent of the present invention is water soluble and yields areporter molecule conjugate with exceptional stability.

One aspect of the present invention provides a compound of Formula IA ora tautomer or salt thereof:

-   -   wherein,    -   L is a linker;    -   R¹ is a halogen;    -   R² is a halogen;    -   R³ comprises a water solubilizing group; and    -   R^(a) is a reporter molecule.

Another aspect of the invention provides a method of making a compoundof Formula I comprising:

-   -   contacting a carrier molecule or a solid support comprising a        nucleophile with a compound of Formula IA or a tautomer or salt        thereof:

-   -   wherein,    -   L is a linker;    -   R¹ is a halogen;    -   R² is a halogen;    -   R³ comprises a water solubilizing group; and    -   R^(a) is a reporter molecule;    -   forming a compound of Formula I or a tautomer or salt thereof:

-   -   wherein,    -   L is the linker;    -   R^(a) is the reporter molecule; and    -   R^(b) is the carrier molecule or solid support comprising a        nucleophile (X).

Another aspect of the invention provides a method of labeling a carriermolecule or solid support comprising:

-   -   contacting the carrier molecule or solid support with a compound        of Formula IA or a tautomer or salt thereof:

-   -   wherein,    -   L is a linker;    -   R¹ is a halogen;    -   R² is a halogen;    -   R³ comprises a water solubilizing group;    -   R^(a) is a reporter molecule; and    -   the carrier molecule or solid support comprises a nucleophile;        and    -   forming a reporter molecule carrier molecule or solid support.    -   Another aspect of the invention provides a method of making a        compound of Formula IA or a tautomer or salt thereof comprising:    -   contacting a compound of Formula IB or a tautomer or salt        thereof:

-   -   with a compound of Formula IC or a tautomer or salt thereof:

-   -   and forming the compound of Formula IA or a tautomer or salt        thereof:

-   -   wherein,    -   R¹ is a halogen;    -   R² is a halogen;    -   R³ comprises a water solubilizing group;    -   L is a linker; and    -   R^(a) is a reporter molecule.

Other objects, features and advantages of the present invention willbecome apparent from the following detailed description. It should beunderstood, however, that the detailed description and the specificexamples, while indicating preferred embodiments of the invention, aregiven by way of illustration only, since various changes andmodifications within the spirit and scope of the invention will becomeapparent to those skilled in the art from this detailed description.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows goat anti-Mouse antibody labeling in 25 mM phosphate bufferpH 8.6 incubated for 1 hour at room temperature.

FIG. 2 shows goat anti-Mouse labeling kinetics in 25 mM phosphate bufferpH 8.6 incubated at room temperature with a molar ratio of 12.

FIG. 3 shows goat anti-Mouse antibody labeling in 25 mM phosphate bufferpH 8.6 incubated at room temperature with the specified compound andmolar ratio. The data shows that Compounds 112 and 122 which contain thedichlorophenol reactive ester react poorly with antibodies for labeling.In contrast, Compounds 102, 108 and 110 which contain thesulfodichlorophenol reactive ester are far superior for antibodylabeling.

FIG. 4 shows ion chromatography with Macro-Prep DEAE Support (Bio-Rad)of Goat anti-Mouse antibody reporter molecule with compound 105, elutedwith a 0-1.0 M NaCl gradient in 20 mM Tris pH 8. The chromatogram showsearly fractions containing under-labeled antibody leading to abroadening of the peak. Under labeled antibodies can lead to decreasedperformance in labeling, detection and visualization activities.

FIG. 5 shows ion chromatography with Macro-Prep DEAE Support (Bio-Rad)of Goat anti-Mouse antibody labeled with compound 120, eluted with a0-1.0 M NaCl gradient in 20 mM Tris pH 8. The chromatogram shows earlyfractions containing unlabeled antibody and a broader peak of labeledantibody. Unlabeled antibodies can lead to decreased performance inlabeling, detection and visualization activities.

FIG. 6 shows ion chromatography with Macro-Prep DEAE Support (Bio-Rad)of Goat anti-Mouse antibody labeled with compound 102, eluted with a0-1.0 M NaCl gradient in 20 mM Tris pH 8. The chromatogram shows anarrower peak of labeled antibody with almost no unlabeled orunderlabeled peaks which can lead to better antibody performance inlabeling, detection and visualization activities.

FIG. 7 shows HPLC (Phenomenex Luna C8 column; eluent: 20 mM TEAA pH 7,gradient 5-95% acetonitrile) trace of the crude reaction mixture ofaminated Panomer-9 random oligonucleotides labeled with an 8-fold excessof compound 102 in borate buffer pH 8.5. The 280 nm trace detects theoligonucleotide while the 495 nm trace detects the dye reportermolecule. The chromatogram is very clean and shows only a few smallreaction side products. The peak before the major peak in the 280 nmtrace is unlabeled Panomer.

FIG. 8 shows HPLC (Phenomenex Luna C8 column; eluent: 20 mM TEAA pH 7,gradient 5-95% acetonitrile) trace of aminated Panomer-9 randomoligonucleotides labeled with an 8-fold excess of compound 105 in boratebuffer pH 8.5 and partially purified by repeated precipitations (4×) inethanol. The 280 nm trace detects the oligonucleotide while the 495 nmtrace detects the dye reporter molecule. The chromatogram shows largeramounts of multiple reaction side products. The peak before the majorpeak in the 280 nm trace is unlabeled Panomer.

DETAILED DESCRIPTION OF THE INVENTION

Introduction

The present invention provides labeling reagents for labeling carriermolecules or solid supports. The labeling reagents of the presentinvention generally include a compound of Formula IA, comprising anester for activation of the reporter molecule. After activation, thereporter molecule is contacted with a carrier molecule or solid supportcomprising at least one nucleophile, such as an amine, thiol or hydroxylgroup wherein a labeled conjugate is formed. The resultant compound isvery stable, thereby providing an excellent method for labeling of abiomolecule such as a protein or polynucleotide. The resultant compoundcan subsequently be added to a biological solution for detection ormonitoring purposes.

The esters described herein have excellent stability properties inaqueous solutions and retain a high degree of reactivity for amines onbiomolecules, making them ideal choices for biomolecule labeling. Thehydrolytic stability has significant impact on the preparation, ease ofhandling, storage stability, and biomolecule labeling efficiency.Additionally, by use of the labeling reagents of the present invention,purification of the molecule is significantly improved and can be doneby silica gel flash chromatography. Column purification is not possiblewith many conventional SE or PFP esters, due to the high reactivity andlow stability of the molecules. The esters of the present invention arealso stable to lyophylization which greatly increases the ease ofhandling and packaging. With greater hydrolytic stability also come lessdegradation upon storage than existing ester modified dyes, such as SEand PFP.

In addition, with more hydrolytic stability comes greater labelingefficiency, with compounds of the present invention giving nearly twiceas much biomolecule labeling as an equivalent amount of SE (see resultsin the Examples section).

Furthermore, the compounds of the present invention have been shown tobe active to biomolecular labeling under a wide range of pH conditions,from pH 6-9. A wide pH reactivity range is a very importantcharacteristic since many biomolecules are unable to be labeled athigher pH due to their limited solubility. This is also advantageous inthe selective N-terminal labeling of proteins which generally occurs ata lower pH range.

Definitions

Before describing the present invention in detail, it is to beunderstood that this invention is not limited to specific compositionsor process steps, as such may vary. It should be noted that, as used inthis specification and the appended claims, the singular form “a”, “an”and “the” include plural references unless the context clearly dictatesotherwise. Thus, for example, reference to “a reporter molecule”includes a plurality of reporter molecules and reference to “an analyte”includes a plurality of analytes and the like.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention is related. The following terms aredefined for purposes of the invention as described herein.

“Alkyl” refers to monovalent saturated aliphatic hydrocarbyl groupshaving from 1 to 10 carbon atoms and preferably 1 to 6 carbon atoms.This term includes, by way of example, linear and branched hydrocarbylgroups such as methyl (CH₃—), ethyl (CH₃CH₂—), n-propyl (CH₃CH₂CH₂—),isopropyl ((CH₃)₂CH—), n-butyl (CH₃CH₂CH₂CH₂—), isobutyl ((CH₃)₂CHCH₂—),sec-butyl ((CH₃)(CH₃CH₂)CH—), t-butyl ((CH₃)₃C—), n-pentyl(CH₃CH₂CH₂CH₂CH₂—), and neopentyl ((CH₃)₃CCH₂—).

“Substituted alkyl” refers to an alkyl group having from 1 to 5,preferably 1 to 3, or more preferably 1 to 2 substituents selected fromthe group consisting of alkoxy, substituted alkoxy, acyl, acylamino,acyloxy, amino, substituted amino, aminocarbonyl, aminothiocarbonyl,aminocarbonylamino, aminothiocarbonylamino, aminocarbonyloxy,aminosulfonyl, aminosulfonyloxy, aminosulfonylamino, amidino, aryl,substituted aryl, aryloxy, substituted aryloxy, arylthio, substitutedarylthio, carboxyl, carboxyl ester, (carboxyl ester)amino, (carboxylester)oxy, cyano, cycloalkyl, substituted cycloalkyl, cycloalkyloxy,substituted cycloalkyloxy, cycloalkylthio, substituted cycloalkylthio,cycloalkenyl, substituted cycloalkenyl, cycloalkenyloxy, substitutedcycloalkenyloxy, cycloalkenylthio, substituted cycloalkenylthio,guanidino, substituted guanidino, halo, hydroxy, heteroaryl, substitutedheteroaryl, heteroaryloxy, substituted heteroaryloxy, heteroarylthio,substituted heteroarylthio, heterocyclic, substituted heterocyclic,heterocyclyloxy, substituted heterocyclyloxy, heterocyclylthio,substituted heterocyclylthio, nitro, SO₃H, substituted sulfonyl,sulfonyloxy, thioacyl, thiol, alkylthio, and substituted alkylthio,wherein said substituents are defined herein.

“Alkoxy” refers to the group —O-alkyl wherein alkyl is defined herein.Alkoxy includes, by way of example, methoxy, ethoxy, n-propoxy,isopropoxy, n-butoxy, t-butoxy, sec-butoxy, and n-pentoxy.

“Substituted alkoxy” refers to the group —O-(substituted alkyl) whereinsubstituted alkyl is defined herein.

“Acyl” refers to the groups H—C(O)—, alkyl-C(O)—, substitutedalkyl-C(O)—, alkenyl-C(O)—, substituted alkenyl-C(O)—, alkynyl-C(O)—,substituted alkynyl-C(O)—, cycloalkyl-C(O)—, substitutedcycloalkyl-C(O)—, cycloalkenyl-C(O)—, substituted cycloalkenyl-C(O)—,aryl-C(O)—, substituted aryl-C(O)—, heteroaryl-C(O)—, substitutedheteroaryl-C(O)—, heterocyclic-C(O)—, and substitutedheterocyclic-C(O)—, wherein alkyl, substituted alkyl, alkenyl,substituted alkenyl, alkynyl, substituted alkynyl, cycloalkyl,substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl,substituted aryl, heteroaryl, substituted heteroaryl, heterocyclic andsubstituted heterocyclic are as defined herein. Acyl includes the“acetyl” group CH₃C(O)—.

“Acylamino” refers to the groups —NRC(O)alkyl, —NRC(O)substituted alkyl,—NRC(O)cycloalkyl, —NRC(O)substituted cycloalkyl, —NRC(O)cycloalkenyl,—NRC(O)substituted cycloalkenyl, —NRC(O)alkenyl, —NRC(O)substitutedalkenyl, —NRC(O)alkynyl, —NRC(O)substituted alkynyl, —NRC(O)aryl,—NRC(O)substituted aryl, —NRC(O)heteroaryl, —NRC(O)substitutedheteroaryl, —NRC(O)heterocyclic, and —NRC(O)substituted heterocyclicwherein R is hydrogen or alkyl and wherein alkyl, substituted alkyl,alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, cycloalkyl,substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl,substituted aryl, heteroaryl, substituted heteroaryl, heterocyclic andsubstituted heterocyclic are as defined herein.

“Acyloxy” refers to the groups alkyl-C(O)O—, substituted alkyl-C(O)O—,alkenyl-C(O)O—, substituted alkenyl-C(O)O—, alkynyl-C(O)O—, substitutedalkynyl-C(O)O—, aryl-C(O)O—, substituted aryl-C(O)O—, cycloalkyl-C(O)O—,substituted cycloalkyl-C(O)O—, cycloalkenyl-C(O)O—, substitutedcycloalkenyl-C(O)O—, heteroaryl-C(O)O—, substituted heteroaryl-C(O)O—,heterocyclic-C(O)O—, and substituted heterocyclic-C(O)O— wherein alkyl,substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substitutedalkynyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substitutedcycloalkenyl, aryl, substituted aryl, heteroaryl, substitutedheteroaryl, heterocyclic, and substituted heterocyclic are as definedherein.

“Amino” refers to the group —NH₂.

“Substituted amino” refers to the group —NR′R″ where R′ and R″ areindependently selected from the group consisting of hydrogen, alkyl,substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substitutedalkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl,cycloalkenyl, substituted cycloalkenyl, heteroaryl, substitutedheteroaryl, heterocyclic, substituted heterocyclic, —SO₂-alkyl,—SO₂-substituted alkyl, —SO₂-alkenyl, —SO₂-substituted alkenyl,—SO₂-cycloalkyl, —SO₂-substituted cylcoalkyl, —SO₂-cycloalkenyl,—SO₂-substituted cylcoalkenyl, —SO₂-aryl, —SO₂-substituted aryl,—SO₂-heteroaryl, —SO₂-substituted heteroaryl, —SO₂-heterocyclic, and—SO₂-substituted heterocyclic and wherein R′ and R″ are optionallyjoined, together with the nitrogen bound thereto to form a heterocyclicor substituted heterocyclic group, provided that R′ and R″ are both nothydrogen, and wherein alkyl, substituted alkyl, alkenyl, substitutedalkenyl, alkynyl, substituted alkynyl, cycloalkyl, substitutedcycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl, substitutedaryl, heteroaryl, substituted heteroaryl, heterocyclic, and substitutedheterocyclic are as defined herein. When R′ is hydrogen and R″ is alkyl,the substituted amino group is sometimes referred to herein asalkylamino. When R′ and R″ are alkyl, the substituted amino group issometimes referred to herein as dialkylamino. When referring to amonosubstituted amino, it is meant that either R′ or R″ is hydrogen butnot both. When referring to a disubstituted amino, it is meant thatneither R′ nor R″ are hydrogen.

“Aminocarbonyl” refers to the group —C(O)NR′R″ where R′ and R″ areindependently selected from the group consisting of hydrogen, alkyl,substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substitutedalkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl,cycloalkenyl, substituted cycloalkenyl, heteroaryl, substitutedheteroaryl, heterocyclic, and substituted heterocyclic and where R′ andR″ are optionally joined together with the nitrogen bound thereto toform a heterocyclic or substituted heterocyclic group, and whereinalkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl,substituted alkynyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl,substituted cycloalkenyl, aryl, substituted aryl, heteroaryl,substituted heteroaryl, heterocyclic and substituted heterocyclic are asdefined herein.

“Aminothiocarbonyl” refers to the group —C(S)NR′R″ where R′ and R″ areindependently selected from the group consisting of hydrogen, alkyl,substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substitutedalkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl,cycloalkenyl, substituted cycloalkenyl, heteroaryl, substitutedheteroaryl, heterocyclic, and substituted heterocyclic and where R′ andR″ are optionally joined together with the nitrogen bound thereto toform a heterocyclic or substituted heterocyclic group, and whereinalkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl,substituted alkynyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl,substituted cycloalkenyl, aryl, substituted aryl, heteroaryl,substituted heteroaryl, heterocyclic and substituted heterocyclic are asdefined herein.

“Aminocarbonylamino” refers to the group —NRC(O)NR′R″ where R ishydrogen or alkyl and R′ and R″ are independently selected from thegroup consisting of hydrogen, alkyl, substituted alkyl, alkenyl,substituted alkenyl, alkynyl, substituted alkynyl, aryl, substitutedaryl, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substitutedcycloalkenyl, heteroaryl, substituted heteroaryl, heterocyclic, andsubstituted heterocyclic and where R′ and R″ are optionally joinedtogether with the nitrogen bound thereto to form a heterocyclic orsubstituted heterocyclic group, and wherein alkyl, substituted alkyl,alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, cycloalkyl,substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl,substituted aryl, heteroaryl, substituted heteroaryl, heterocyclic andsubstituted heterocyclic are as defined herein.

“Aminothiocarbonylamino” refers to the group —NRC(S)NR′R″ where R ishydrogen or alkyl and R′ and R″ are independently selected from thegroup consisting of hydrogen, alkyl, substituted alkyl, alkenyl,substituted alkenyl, alkynyl, substituted alkynyl, aryl, substitutedaryl, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substitutedcycloalkenyl, heteroaryl, substituted heteroaryl, heterocyclic, andsubstituted heterocyclic and where R′ and R″ are optionally joinedtogether with the nitrogen bound thereto to form a heterocyclic orsubstituted heterocyclic group, and wherein alkyl, substituted alkyl,alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, cycloalkyl,substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl,substituted aryl, heteroaryl, substituted heteroaryl, heterocyclic andsubstituted heterocyclic are as defined herein.

“Aminocarbonyloxy” refers to the group —O—C(O)NR′R″ where R′ and R″ areindependently selected from the group consisting of hydrogen, alkyl,substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substitutedalkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl,cycloalkenyl, substituted cycloalkenyl, heteroaryl, substitutedheteroaryl, heterocyclic, and substituted heterocyclic and where R′ andR″ are optionally joined together with the nitrogen bound thereto toform a heterocyclic or substituted heterocyclic group, and whereinalkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl,substituted alkynyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl,substituted cycloalkenyl, aryl, substituted aryl, heteroaryl,substituted heteroaryl, heterocyclic and substituted heterocyclic are asdefined herein.

“Aminosulfonyl” refers to the group —SO₂NR′R″ where R′ and R″ areindependently selected from the group consisting of hydrogen, alkyl,substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substitutedalkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl,cycloalkenyl, substituted cycloalkenyl, heteroaryl, substitutedheteroaryl, heterocyclic, and substituted heterocyclic and where R′ andR″ are optionally joined together with the nitrogen bound thereto toform a heterocyclic or substituted heterocyclic group, and whereinalkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl,substituted alkynyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl,substituted cycloalkenyl, aryl, substituted aryl, heteroaryl,substituted heteroaryl, heterocyclic and substituted heterocyclic are asdefined herein.

“Aminosulfonyloxy” refers to the group —O—SO₂NR′R″ where R′ and R″ areindependently selected from the group consisting of hydrogen, alkyl,substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substitutedalkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl,cycloalkenyl, substituted cycloalkenyl, heteroaryl, substitutedheteroaryl, heterocyclic, and substituted heterocyclic and where R′ andR″ are optionally joined together with the nitrogen bound thereto toform a heterocyclic or substituted heterocyclic group, and whereinalkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl,substituted alkynyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl,substituted cycloalkenyl, aryl, substituted aryl, heteroaryl,substituted heteroaryl, heterocyclic and substituted heterocyclic are asdefined herein.

“Aminosulfonylamino” refers to the group —NR—SO₂NR′R″ where R ishydrogen or alkyl and R′ and R″ are independently selected from thegroup consisting of hydrogen, alkyl, substituted alkyl, alkenyl,substituted alkenyl, alkynyl, substituted alkynyl, aryl, substitutedaryl, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substitutedcycloalkyenyl, heteroaryl, substituted heteroaryl, heterocyclic, andsubstituted heterocyclic and where R′ and R″ are optionally joinedtogether with the nitrogen bound thereto to form a heterocyclic orsubstituted heterocyclic group, and wherein alkyl, substituted alkyl,alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, cycloalkyl,substituted cycloalkyl, cycloalkenyl, substituted cycloalkyenyl, aryl,substituted aryl, heteroaryl, substituted heteroaryl, heterocyclic andsubstituted heterocyclic are as defined herein.

“Amidino” refers to the group —C(═NR″)R′R″ where R′, R″, and R′″ areindependently selected from the group consisting of hydrogen, alkyl,substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substitutedalkynyl, aryl, substituted aryl, cycloalkyl, substituted cycloalkyl,cycloalkenyl, substituted cycloalkenyl, heteroaryl, substitutedheteroaryl, heterocyclic, and substituted heterocyclic and where R′ andR″ are optionally joined together with the nitrogen bound thereto toform a heterocyclic or substituted heterocyclic group, and whereinalkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl,substituted alkynyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl,substituted cycloalkenyl, aryl, substituted aryl, heteroaryl,substituted heteroaryl, heterocyclic and substituted heterocyclic are asdefined herein.

“Aryl” or “Ar” refers to a monovalent aromatic carbocyclic group of from6 to 14 carbon atoms having a single ring (e.g., phenyl) or multiplecondensed rings (e.g., naphthyl or anthryl) which condensed rings may ormay not be aromatic (e.g., 2-benzoxazolinone,2H-1,4-benzoxazin-3(4H)-one-7-yl, and the like) provided that the pointof attachment is at an aromatic carbon atom. Preferred aryl groupsinclude phenyl and naphthyl.

“Substituted aryl” refers to aryl groups which are substituted with 1 to5, preferably 1 to 3, or more preferably 1 to 2 substituents selectedfrom the group consisting of alkyl, substituted alkyl, alkenyl,substituted alkenyl, alkynyl, substituted alkynyl, alkoxy, substitutedalkoxy, acyl, acylamino, acyloxy, amino, substituted amino,aminocarbonyl, aminothiocarbonyl, aminocarbonylamino,aminothiocarbonylamino, aminocarbonyloxy, aminosulfonyl,aminosulfonyloxy, aminosulfonylamino, amidino, aryl, substituted aryl,aryloxy, substituted aryloxy, arylthio, substituted arylthio, carboxyl,carboxyl ester, (carboxyl ester)amino, (carboxyl ester)oxy, cyano,cycloalkyl, substituted cycloalkyl, cycloalkyloxy, substitutedcycloalkyloxy, cycloalkylthio, substituted cycloalkylthio, cycloalkenyl,substituted cycloalkenyl, cycloalkenyloxy, substituted cycloalkenyloxy,cycloalkenylthio, substituted cycloalkenylthio, guanidino, substitutedguanidino, halo, hydroxy, heteroaryl, substituted heteroaryl,heteroaryloxy, substituted heteroaryloxy, heteroarylthio, substitutedheteroarylthio, heterocyclic, substituted heterocyclic, heterocyclyloxy,substituted heterocyclyloxy, heterocyclylthio, substitutedheterocyclylthio, nitro, SO₃H, substituted sulfonyl, sulfonyloxy,thioacyl, thiol, alkylthio, and substituted alkylthio, wherein saidsubstituents are defined herein.

“Aryloxy” refers to the group —O-aryl, where aryl is as defined herein,that includes, by way of example, phenoxy and naphthoxy.

“Substituted aryloxy” refers to the group —O-(substituted aryl) wheresubstituted aryl is as defined herein.

“Arylthio” refers to the group —S-aryl, where aryl is as defined herein.

“Substituted arylthio” refers to the group —S-(substituted aryl), wheresubstituted aryl is as defined herein.

“Alkenyl” refers to alkenyl groups having from 2 to 6 carbon atoms andpreferably 2 to 4 carbon atoms and having at least 1 and preferably from1 to 2 sites of alkenyl unsaturation. Such groups are exemplified, forexample, by vinyl, allyl, and but-3-en-1-yl.

“Substituted alkenyl” refers to alkenyl groups having from 1 to 3substituents, and preferably 1 to 2 substituents, selected from thegroup consisting of alkoxy, substituted alkoxy, acyl, acylamino,acyloxy, amino, substituted amino, aminocarbonyl, aminothiocarbonyl,aminocarbonylamino, aminothiocarbonylamino, aminocarbonyloxy,aminosulfonyl, aminosulfonyloxy, aminosulfonylamino, amidino, aryl,substituted aryl, aryloxy, substituted aryloxy, arylthio, substitutedarylthio, carboxyl, carboxyl ester, (carboxyl ester)amino, (carboxylester)oxy, cyano, cycloalkyl, substituted cycloalkyl, cycloalkyloxy,substituted cycloalkyloxy, cycloalkylthio, substituted cycloalkylthio,cycloalkenyl, substituted cycloalkenyl, cycloalkenyloxy, substitutedcycloalkenyloxy, cycloalkenylthio, substituted cycloalkenylthio,guanidino, substituted guanidino, halo, hydroxy, heteroaryl, substitutedheteroaryl, heteroaryloxy, substituted heteroaryloxy, heteroarylthio,substituted heteroarylthio, heterocyclic, substituted heterocyclic,heterocyclyloxy, substituted heterocyclyloxy, heterocyclylthio,substituted heterocyclylthio, nitro, SO₃H, substituted sulfonyl,sulfonyloxy, thioacyl, thiol, alkylthio, and substituted alkylthio,wherein said substituents are defined herein and with the proviso thatany hydroxy substitution is not attached to a vinyl (unsaturated) carbonatom.

“Alkynyl” refers to alkynyl groups having from 2 to 6 carbon atoms andpreferably 2 to 3 carbon atoms and having at least 1 and preferably from1 to 2 sites of alkynyl unsaturation.

“Substituted alkynyl” refers to alkynyl groups having from 1 to 3substituents, and preferably 1 to 2 substituents, selected from thegroup consisting of alkoxy, substituted alkoxy, acyl, acylamino,acyloxy, amino, substituted amino, aminocarbonyl, aminothiocarbonyl,aminocarbonylamino, aminothiocarbonylamino, aminocarbonyloxy,aminosulfonyl, aminosulfonyloxy, aminosulfonylamino, amidino, aryl,substituted aryl, aryloxy, substituted aryloxy, arylthio, substitutedarylthio, carboxyl, carboxyl ester, (carboxyl ester)amino, (carboxylester)oxy, cyano, cycloalkyl, substituted cycloalkyl, cycloalkyloxy,substituted cycloalkyloxy, cycloalkylthio, substituted cycloalkylthio,cycloalkenyl, substituted cycloalkenyl, cycloalkenyloxy, substitutedcycloalkenyloxy, cycloalkenylthio, substituted cycloalkenylthio,guanidino, substituted guanidino, halo, hydroxy, heteroaryl, substitutedheteroaryl, heteroaryloxy, substituted heteroaryloxy, heteroarylthio,substituted heteroarylthio, heterocyclic, substituted heterocyclic,heterocyclyloxy, substituted heterocyclyloxy, heterocyclylthio,substituted heterocyclylthio, nitro, SO₃H, substituted sulfonyl,sulfonyloxy, thioacyl, thiol, alkylthio, and substituted alkylthio,wherein said substituents are defined herein and with the proviso thatany hydroxy substitution is not attached to an acetylenic carbon atom.

“Azenyl” refers to the group —N═NH. “Substituted azenyl” refers to—N═NR′, wherein R′ is alkyl, substituted alkyl, amino (i.e. triazenyl),imino (azide), substituted amino, alkenyl, substituted alkenyl, alkynyl,substituted alkynyl, aryl, substituted aryl, cycloalkyl, substitutedcycloalkyl, cycloalkenyl, substituted cycloalkenyl, heteroaryl,substituted heteroaryl, heterocyclic, or a substituted heterocyclicgroup.

“Carbonyl” refers to the divalent group —C(O)— which is equivalent to—C(═O)—.

“Carboxyl” or “carboxy” refers to —COOH or salts thereof.

“Carboxyl ester” or “carboxy ester” refers to the groups —C(O)O-alkyl,—C(O)O-substituted alkyl, —C(O)O-alkenyl, —C(O)O-substituted alkenyl,—C(O)O-alkynyl, —C(O)O-substituted alkynyl, —C(O)O-aryl,—C(O)O-substituted aryl, —C(O)O-cycloalkyl, —C(O)O-substitutedcycloalkyl, —C(O)O-cycloalkenyl, —C(O)O-substituted cycloalkenyl,—C(O)O-heteroaryl, —C(O)O-substituted heteroaryl, —C(O)O-heterocyclic,and —C(O)O-substituted heterocyclic wherein alkyl, substituted alkyl,alkenyl, substituted alkenyl, alkynyl, substituted alkynyl, cycloalkyl,substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl,substituted aryl, heteroaryl, substituted heteroaryl, heterocyclic, andsubstituted heterocyclic are as defined herein.

“(Carboxyl ester)amino” refers to the group —NR—C(O)O-alkyl, substituted—NR—C(O)O-alkyl, —NR—C(O)O-alkenyl, —NR—C(O)O-substituted alkenyl,—NR—C(O)O-alkynyl, —NR—C(O)O-substituted alkynyl, —NR—C(O)O-aryl,—NR—C(O)O-substituted aryl, —NR—C(O)O-cycloalkyl, —NR—C(O)O-substitutedcycloalkyl, —NR—C(O)O-cycloalkenyl, —NR—C(O)O-substituted cycloalkenyl,—NR—C(O)O-heteroaryl, —NR—C(O)O-substituted heteroaryl,—NR—C(O)O-heterocyclic, and —NR—C(O)O-substituted heterocyclic wherein Ris alkyl or hydrogen, and wherein alkyl, substituted alkyl, alkenyl,substituted alkenyl, alkynyl, substituted alkynyl, cycloalkyl,substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl,substituted aryl, heteroaryl, substituted heteroaryl, heterocyclic, andsubstituted heterocyclic are as defined herein.

“(Carboxyl ester)oxy” refers to the group —O—C(O)O-alkyl, substituted—O—C(O)O-alkyl, —O—C(O)O-alkenyl, —O—C(O)O-substituted alkenyl,—O—C(O)O-alkynyl, —O—C(O)O-substituted alkynyl, —O—C(O)O-aryl,—O—C(O)O-substituted aryl, —O—C(O)O-cycloalkyl, —O—C(O)O-substitutedcycloalkyl, —O—C(O)O-cycloalkenyl, —O—C(O)O-substituted cycloalkenyl,—O—C(O)O-heteroaryl, —O—C(O)O-substituted heteroaryl,—O—C(O)O-heterocyclic, and —O—C(O)O-substituted heterocyclic whereinalkyl, substituted alkyl, alkenyl, substituted alkenyl, alkynyl,substituted alkynyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl,substituted cycloalkenyl, aryl, substituted aryl, heteroaryl,substituted heteroaryl, heterocyclic, and substituted heterocyclic areas defined herein.

“Cyano” refers to the group —CN.

“Cycloalkyl” refers to cyclic alkyl groups of from 3 to 10 carbon atomshaving single or multiple cyclic rings including fused, bridged, andspiro ring systems. Examples of suitable cycloalkyl groups include, forinstance, adamantyl, cyclopropyl, cyclobutyl, cyclopentyl, andcyclooctyl.

“Cycloalkenyl” refers to non-aromatic cyclic alkyl groups of from 3 to10 carbon atoms having single or multiple cyclic rings and having atleast one >C═C<ring unsaturation and preferably from 1 to 2 sitesof >C═C<ring unsaturation.

“Substituted cycloalkyl” and “substituted cycloalkenyl” refers to acycloalkyl or cycloalkenyl group having from 1 to 5 or preferably 1 to 3substituents selected from the group consisting of oxo, thione, alkyl,substituted alkyl, alkenyl, substituted alkenyl, alkynyl, substitutedalkynyl, alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino,substituted amino, aminocarbonyl, aminothiocarbonyl, aminocarbonylamino,aminothiocarbonylamino, aminocarbonyloxy, aminosulfonyl,aminosulfonyloxy, aminosulfonylamino, amidino, aryl, substituted aryl,aryloxy, substituted aryloxy, arylthio, substituted arylthio, carboxyl,carboxyl ester, (carboxyl ester)amino, (carboxyl ester)oxy, cyano,cycloalkyl, substituted cycloalkyl, cycloalkyloxy, substitutedcycloalkyloxy, cycloalkylthio, substituted cycloalkylthio, cycloalkenyl,substituted cycloalkenyl, cycloalkenyloxy, substituted cycloalkenyloxy,cycloalkenylthio, substituted cycloalkenylthio, guanidino, substitutedguanidino, halo, hydroxy, heteroaryl, substituted heteroaryl,heteroaryloxy, substituted heteroaryloxy, heteroarylthio, substitutedheteroarylthio, heterocyclic, substituted heterocyclic, heterocyclyloxy,substituted heterocyclyloxy, heterocyclylthio, substitutedheterocyclylthio, nitro, SO₃H, substituted sulfonyl, sulfonyloxy,thioacyl, thiol, alkylthio, and substituted alkylthio, wherein saidsubstituents are defined herein.

“Cycloalkyloxy” refers to —O-cycloalkyl.

“Substituted cycloalkyloxy refers to —O-(substituted cycloalkyl).

“Cycloalkylthio” refers to —S-cycloalkyl.

“Substituted cycloalkylthio” refers to —S-(substituted cycloalkyl).

“Cycloalkenyloxy” refers to —O-cycloalkenyl.

“Substituted cycloalkenyloxy refers to —O-(substituted cycloalkenyl).

“Cycloalkenylthio” refers to —S-cycloalkenyl.

“Substituted cycloalkenylthio” refers to —S-(substituted cycloalkenyl).

“Guanidino” refers to the group —NHC(═NH)NH₂.

“Substituted guanidino” refers to —NR¹³C(═NR¹³)N(R¹³)₂ where each R¹³ isindependently selected from the group consisting of hydrogen, alkyl,substituted alkyl, aryl, substituted aryl, heteroaryl, substitutedheteroaryl, heterocyclic, and substituted heterocyclic and two R¹³groups attached to a common guanidino nitrogen atom are optionallyjoined together with the nitrogen bound thereto to form a heterocyclicor substituted heterocyclic group, provided that at least one R¹³ is nothydrogen, and wherein said substituents are as defined herein.

“H” indicates hydrogen.

“Halo” or “halogen” refers to fluoro, chloro, bromo and iodo.

“Hydroxy” or “hydroxyl” refers to the group —OH.

“Heteroaryl” refers to an aromatic group of from 1 to 10 carbon atomsand 1 to 4 heteroatoms selected from the group consisting of oxygen,nitrogen and sulfur within the ring. Such heteroaryl groups can have asingle ring (e.g., pyridinyl or furyl) or multiple condensed rings(e.g., indolizinyl or benzothienyl) wherein the condensed rings may ormay not be aromatic and/or contain a heteroatom provided that the pointof attachment is through an atom of the aromatic heteroaryl group. Inone embodiment, the nitrogen and/or the sulfur ring atom(s) of theheteroaryl group are optionally oxidized to provide for the N-oxide(N→O), sulfinyl, or sulfonyl moieties. Preferred heteroaryls includepyridinyl, pyrrolyl, indolyl, thiophenyl, and furanyl.

“Substituted heteroaryl” refers to heteroaryl groups that aresubstituted with from 1 to 5, preferably 1 to 3, or more preferably 1 to2 substituents selected from the group consisting of the same group ofsubstituents defined for substituted aryl.

“Heteroaryloxy” refers to —O-heteroaryl.

“Substituted heteroaryloxy refers to the group —O-(substitutedheteroaryl).

“Heteroarylthio” refers to the group —S-heteroaryl.

“Substituted heteroarylthio” refers to the group —S-(substitutedheteroaryl).

“Heterocycle” or “heterocyclic” or “heterocycloalkyl” or “heterocyclyl”refers to a saturated or unsaturated group having a single ring ormultiple condensed rings, including fused bridged and spiro ringsystems, from 1 to 10 carbon atoms and from 1 to 4 hetero atoms selectedfrom the group consisting of nitrogen, sulfur or oxygen within the ringwherein, in fused ring systems, one or more the rings can be cycloalkyl,aryl or heteroaryl provided that the point of attachment is through thenon-aromatic ring. In one embodiment, the nitrogen and/or sulfur atom(s)of the heterocyclic group are optionally oxidized to provide for theN-oxide, sulfinyl, sulfonyl moieties.

“Substituted heterocyclic” or “substituted heterocycloalkyl” or“substituted heterocyclyl” refers to heterocyclyl groups that aresubstituted with from 1 to 5 or preferably 1 to 3 of the samesubstituents as defined for substituted cycloalkyl.

“Heterocyclyloxy” refers to the group —O-heterocycyl.

“Substituted heterocyclyloxy refers to the group —O-(substitutedheterocycyl).

“Heterocyclylthio” refers to the group —S-heterocycyl.

“Substituted heterocyclylthio” refers to the group —S-(substitutedheterocycyl).

Examples of heterocycle and heteroaryls include, but are not limited to,azetidine, pyrrole, imidazole, pyrazole, pyridine, pyrazine, pyrimidine,pyridazine, indolizine, isoindole, indole, dihydroindole, indazole,purine, quinolizine, isoquinoline, quinoline, phthalazine,naphthylpyridine, quinoxaline, quinazoline, cinnoline, pteridine,carbazole, carboline, phenanthridine, acridine, phenanthroline,isothiazole, phenazine, isoxazole, phenoxazine, phenothiazine,imidazolidine, imidazoline, piperidine, piperazine, indoline,phthalimide, 1,2,3,4-tetrahydroisoquinoline,4,5,6,7-tetrahydrobenzo[b]thiophene, thiazole, thiazolidine, thiophene,benzo[b]thiophene, morpholinyl, thiomorpholinyl (also referred to asthiamorpholinyl), 1,1-dioxothiomorpholinyl, piperidinyl, pyrrolidine,and tetrahydrofuranyl.

“Hydrazinyl” refers to the group —NHNH₂—, ═NNH—, or ═N⁽⁺⁾HNH₂—.

“Substituted hydrazinyl” refers to a hydrazinyl group, wherein anon-hydrogen atom, such as an alkyl group, is appended to one or both ofthe hydrazinyl amine groups. An example of substituted hydrazinyl is—N(alkyl)-NH₂ or ═N⁺(alkyl)-NH₂.

“Nitro” refers to the group —NO₂.

“Oxo” refers to the atom (═O) or (—O⁻).

“Spirocyclyl” refers to divalent saturated cyclic group from 3 to 10carbon atoms having a cycloalkyl or heterocyclyl ring with a spiro union(the union formed by a single atom which is the only common member ofthe rings) as exemplified by the following structure:

“Sulfonyl” refers to the divalent group —S(O)₂—.

“Substituted sulfonyl” refers to the group —SO₂-alkyl, —SO₂-substitutedalkyl, —SO₂-alkenyl, —SO₂-substituted alkenyl, —SO₂-cycloalkyl,—SO₂-substituted cylcoalkyl, —SO₂-cycloalkenyl, —SO₂-substitutedcylcoalkenyl, —SO₂-aryl, —SO₂-substituted aryl, —SO₂-heteroaryl,—SO₂-substituted heteroaryl, —SO₂-heterocyclic, —SO₂-substitutedheterocyclic, wherein alkyl, substituted alkyl, alkenyl, substitutedalkenyl, alkynyl, substituted alkynyl, cycloalkyl, substitutedcycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl, substitutedaryl, heteroaryl, substituted heteroaryl, heterocyclic and substitutedheterocyclic are as defined herein. Substituted sulfonyl includes groupssuch as methyl-SO₂—, phenyl-SO₂—, and 4-methylphenyl-SO₂—.

“Sulfonyloxy” refers to the group —OSO₂-alkyl, —OSO₂-substituted alkyl,—OSO₂-alkenyl, —OSO₂-substituted alkenyl, —OSO₂-cycloalkyl,—OSO₂-substituted cylcoalkyl, —OSO₂-cycloalkenyl, —OSO₂-substitutedcylcoalkenyl, —OSO₂-aryl, —OSO₂-substituted aryl, —OSO₂-heteroaryl,—OSO₂-substituted heteroaryl, —OSO₂-heterocyclic, —OSO₂-substitutedheterocyclic, wherein alkyl, substituted alkyl, alkenyl, substitutedalkenyl, alkynyl, substituted alkynyl, cycloalkyl, substitutedcycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl, substitutedaryl, heteroaryl, substituted heteroaryl, heterocyclic and substitutedheterocyclic are as defined herein.

“Thioacyl” refers to the groups H—C(S)—, alkyl-C(S)—, substitutedalkyl-C(S)—, alkenyl-C(S)—, substituted alkenyl-C(S)—, alkynyl-C(S)—,substituted alkynyl-C(S)—, cycloalkyl-C(S)—, substitutedcycloalkyl-C(S)—, cycloalkenyl-C(S)—, substituted cycloalkenyl-C(S)—,aryl-C(S)—, substituted aryl-C(S)—, heteroaryl-C(S)—, substitutedheteroaryl-C(S)—, heterocyclic-C(S)—, and substitutedheterocyclic-C(S)—, wherein alkyl, substituted alkyl, alkenyl,substituted alkenyl, alkynyl, substituted alkynyl, cycloalkyl,substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl,substituted aryl, heteroaryl, substituted heteroaryl, heterocyclic andsubstituted heterocyclic are as defined herein.

“Thiol” refers to the group —SH.

“Thiocarbonyl” refers to the divalent group —C(S)— which is equivalentto —C(═S)—.

“Thione” refers to the atom (═S).

“Alkylthio” refers to the group —S-alkyl wherein alkyl is as definedherein.

“Substituted alkylthio” refers to the group —S-(substituted alkyl)wherein substituted alkyl is as defined herein.

A squiggly line intersecting a bond, such as:

indicates the point of attachment to the base molecule, wherein in theabove structure the point of attachment is any unoccupied position onthe phenyl ring.

“Stereoisomer” or “stereoisomers” refer to compounds that differ in thechirality of one or more stereocenters. Stereoisomers includeenantiomers and diastereomers.

“Tautomer” refers to alternate forms of a compound that differ in theposition of a proton, such as enol-keto and imine-enamine tautomers, orthe tautomeric forms of heteroaryl groups containing a ring atomattached to both a ring —NH— moiety and a ring ═N— moeity such aspyrazoles, imidazoles, benzimidazoles, triazoles, and tetrazoles.

Unless indicated otherwise, the nomenclature of substituents that arenot explicitly defined herein are arrived at by naming the terminalportion of the functionality followed by the adjacent functionalitytoward the point of attachment. For example, the substituent“arylalkyloxycabonyl” refers to the group (aryl)-(alkyl)-O—C(O)—.

It is understood that in all substituted groups defined above, polymersarrived at by defining substituents with further substituents tothemselves (e.g., substituted aryl having a substituted aryl group as asubstituent which is itself substituted with a substituted aryl group,which is further substituted by a substituted aryl group etc.) are notintended for inclusion herein. In such cases, the maximum number of suchsubstitutions is three. For example, serial substitutions of substitutedaryl groups with two other substituted aryl groups are limited to-substituted aryl-(substituted aryl)-substituted aryl.

Similarly, it is understood that the above definitions are not intendedto include impermissible substitution patterns (e.g., methyl substitutedwith 5 fluoro groups). Such impermissible substitution patterns are wellknown to the skilled artisan.

“Salt” refers to acceptable salts of a compound, which salts are derivedfrom a variety of organic and inorganic counter ions well known in theart and include, by way of example only, sodium, potassium, calcium,magnesium, ammonium, and tetraalkylammonium; and when the moleculecontains a basic functionality, salts of organic or inorganic acids,such as hydrochloride, hydrobromide, tartrate, mesylate, acetate,maleate, and oxalate.

The terms “protein” and “polypeptide” are used herein in a generic senseto include polymers of amino acid residues of any length. The term“peptide” is used herein to refer to polypeptides having less than 250amino acid residues, typically less than 100 amino acid residues. Theterms apply to amino acid polymers in which one or more amino acidresidues are an artificial chemical analogue of a correspondingnaturally occurring amino acid, as well as to naturally occurring aminoacid polymers.

A “water solubilizing group” as used herein indicates a polar and/orcharged, preferably anionic, substituent that increases water solubilityof a base molecule. Water solubilizing groups may be appended directlyto the base molecule, or through a linker. Water solubilizing groups ofthe present invention include carboxyl groups, sulphonic acids, hydroxylgroups, substituted azenyl groups, polyoxyalkylene (such as PEG),phosphate groups, bisphosphonate groups, or substitutions that introducean additional net charge and/or polarity into the molecule.

The term “reactive group” as used herein refers to a group that iscapable of reacting with another chemical group to form a covalent bond,i.e. is covalently reactive under suitable reaction conditions, andgenerally represents a point of attachment for another substance. In thepresent invention the labeling reagents comprise a reactive groupaccording to Formula IA and the carrier molecule or solid supportcomprises at least one suitable nucleophile that will react with thereactive group according to Formula IA to form a covalent bond.

The term “detectable response” as used herein refers to an occurrence ofor a change in, a signal that is directly or indirectly detectableeither by observation or by instrumentation. Typically, the detectableresponse is an optical response resulting in a change in the wavelengthdistribution patterns or intensity of absorbance or fluorescence or achange in light scatter, fluorescence lifetime, fluorescencepolarization, or a combination of the above parameters.

The term “dye” as used herein refers to a compound that emits light toproduce an observable detectable signal.

The term “fluorophore” or “fluorogenic” as used herein refers to acomposition that demonstrates a change in fluorescence upon binding to abiological compound or analyte interest. Preferred fluorophores of thepresent invention include fluorescent dyes having a high quantum yieldin aqueous media. Exemplary fluorophores include xanthene, indole,borapolyazaindacene, furan, and benzofuran, among others. Thefluorophores of the present invention may be substituted to alter thesolubility, spectral properties or physical properties of thefluorophore.

The term “carrier molecule” as used herein refers to a biological or anon-biological component that can be covalently bonded to a labelingreagent of the present invention. Such components include, but are notlimited to, an amino acid, a peptide, a protein, a polysaccharide, anucleoside, a nucleotide, an oligonucleotide, a nucleic acid, a hapten,a psoralen, a drug, a hormone, a lipid, a lipid assembly, a syntheticpolymer, a polymeric microparticle, a biological cell, a virus andcombinations thereof. As used herein carrier molecules comprise anucleophile for reaction with the present labeling reagents. Carriermolecules are described in greater detail below.

“Covalently bonded” as used herein indicates a direct covalent linkageor through a number of atoms corresponding to a linker moiety.

The term “reporter molecule” as used herein refers to a chemical moietyor protein that retains it's native properties (e.g. spectralproperties, conformation and activity) when part of a labeling reagentof the present invention and used in the present methods. Illustrativereporter molecules can be directly detectable (fluorophore) orindirectly detectable (hapten or enzyme). Such reporter moleculesinclude, but are not limited to, radio reporter molecules that can bemeasured with radiation-counting devices; pigments, dyes or otherchromogens that can be visually observed or measured with aspectrophotometer; spin labels that can be measured with a spin labelanalyzer; and fluorescent moieties, where the output signal is generatedby the excitation of a suitable molecular adduct and that can bevisualized by excitation with light that is absorbed by the dye or canbe measured with standard fluorometers or imaging systems, for example.The reporter molecule can be a luminescent substance such as a phosphoror fluorogen; a bioluminescent substance; a chemiluminescent substance,where the output signal is generated by chemical modification of thesignal compound; a metal-containing substance; or an enzyme, where thereoccurs an enzyme-dependent secondary generation of signal, such as theformation of a colored product from a colorless substrate. The reportermolecule may also take the form of a chemical or biochemical, or aninert particle, including but not limited to colloidal gold,microspheres, quantum dots, or inorganic crystals such as nanocrystalsor phosphors (see, e.g., Beverloo, et al., Anal. Biochem. 203, 326-34(1992)). The term reporter molecule can also refer to a “tag” or haptenthat can bind selectively to a labeled molecule such that the labeledmolecule, when added subsequently, is used to generate a detectablesignal. For instance, one can use biotin, iminobiotin or desthiobiotinas a tag and then use an avidin or streptavidin conjugate of horseradishperoxidase (HRP) to bind to the tag, and then use a chromogenicsubstrate (e.g., tetramethylbenzidine) or a fluorogenic substrate suchas Amplex Red or Amplex Gold (Molecular Probes, Inc.) to detect thepresence of HRP. In a similar fashion, the tag can be a hapten orantigen (e.g., digoxigenin), and an enzymatically, fluorescently, orradioactively labeled antibody can be used to bind to the tag. Numerousreporter molecules are known by those of skill in the art and include,but are not limited to, particles, fluorescent dyes, haptens, enzymesand their chromogenic, fluorogenic, and chemiluminescent substrates, andother reporter molecules that are described in the MOLECULAR PROBESHANDBOOK OF FLUORESCENT PROBES AND RESEARCH CHEMICALS by Richard P.Haugland, 10^(th) Ed., (2005), the contents of which are incorporated byreference, and in other published sources. As used herein a reportermolecule is not an amino acid.

The term “Labeling Reagent” as used herein refers to present compoundthat comprises a reporter molecule and a reactive group accordingFormula IA.

The term “Linker” as used herein, refers to a single covalent bond or aseries of stable covalent bonds incorporating 1-20 nonhydrogen atomsselected from the group consisting of C, N, O, S and P. The presentlabeling reagent may comprise a linker that covalently attaches thereporter molecule to the reactive group according to Formula IA or to acarrier group or solid support. Exemplary linking members include amoiety that includes —C(O)NH—, —C(O)O—, —NH—, —S—, —O—, and the like. A“cleavable linker” is a linker that has one or more cleavable groupsthat may be broken by the result of a reaction or condition. The term“cleavable group” refers to a moiety that allows for release of aportion, e.g., a fluorogenic or fluorescent moiety, of a conjugate fromthe remainder of the conjugate by cleaving a bond linking the releasedmoiety to the remainder of the conjugate. Such cleavage is eitherchemical in nature, or enzymatically mediated. Exemplary enzymaticallycleavable groups include natural amino acids or peptide sequences thatend with a natural amino acid.

In addition to enzymatically cleavable groups, it is within the scope ofthe present invention to include one or more sites that are cleaved bythe action of an agent other than an enzyme. Exemplary non-enzymaticcleavage agents include, but are not limited to, acids, bases, light(e.g., nitrobenzyl derivatives, phenacyl groups, benzoin esters), andheat. Many cleaveable groups are known in the art. See, for example,Jung et al., Biochem. Biophys. Acta, 761: 152-162 (1983); Joshi et al.,J. Biol. Chem., 265: 14518-14525 (1990); Zarling et al., J. Immunol.,124: 913-920 (1980); Bouizar et al., Eur. J. Biochem., 155: 141-147(1986); Park et al., J. Biol. Chem., 261: 205-210 (1986); Browning etal., J. Immunol., 143: 1859-1867 (1989). Moreover a broad range ofcleavable, bifunctional (both homo- and hetero-bifunctional) spacer armsare commercially available.

An exemplary cleavable group, an ester, is cleavable group that may becleaved by a reagent, e.g. sodium hydroxide, resulting in acarboxylate-containing fragment and a hydroxyl-containing product.

The term “sample” as used herein refers to any material that may containan analyte of interest, as defined below, or a carrier molecule or solidsupport of the present invention. Typically, the sample comprises apopulation of cells, cellular extract, subcellular components, tissueculture, a bodily fluid, and tissue. The sample may be in an aqueoussolution, a viable cell culture or immobilized on a solid or semi solidsurface such as a gel, a membrane, a glass surface, a microparticle oron a microarray.

The term “solid support” as used here refers to a matrix or media thatis substantially insoluble in liquid phases and capable of binding amolecule or particle of interest. Solid supports of the currentinvention include semi-solid supports and are not limited to a specifictype of support. Useful solid supports include solid and semi-solidmatrixes, such as aerogels and hydrogels, resins, beads, biochips(including thin film coated biochips), microfluidic chip, a siliconchip, multi-well plates (also referred to as microtitre plates ormicroplates), membranes, conducting and nonconducting metals, glass(including microscope slides) and magnetic supports. More specificexamples of useful solid supports include silica gels, polymericmembranes, particles, derivatized plastic films, glass beads, cotton,plastic beads, alumina gels, polysaccharides such as Sepharose,poly(acrylate), polystyrene, poly(acrylamide), polyol, agarose, agar,cellulose, dextran, starch, FICOLL, heparin, glycogen, amylopectin,mannan, inulin, nitrocellulose, diazocellulose, polyvinylchloride,polypropylene, polyethylene (including poly(ethylene glycol)), nylon,latex bead, magnetic bead, paramagnetic bead, superparamagnetic bead,starch and the like.

The Labeling Reagents

In accordance with the present invention, labeling reagents, methods forlabeling carrier molecules or solid support and methods for using thelabeled conjugates to detect an analyte of interest in a sample areprovided. The labeling reagents comprise a reporter molecule, as definedherein, and a reactive group according to Formula IA, as defined below.The labeling reagents are then used to label a wide range of carriermolecules and solid supports by methods well known in the art and usedin a wide range of assays and applications for the detection of aparticular analyte.

Labeling Reagents

One aspect of the present invention provides a compound of Formula IA ora tautomer or salt thereof:

-   -   wherein,    -   L is a linker;    -   R¹ is a halogen;    -   R² is a halogen;    -   R³ comprises a water solubilizing group; and    -   R^(a) is a reporter molecule.

In another more particular embodiment, L is a covalent bond, -alkyl-,-substituted alkyl-, -alkenyl-, -substituted alkenyl-, -heterocyclyl-,-substituted heterocyclyl-, -aryl-, -substituted aryl-, -heteroaryl-,-substituted heteroaryl-, -cycloakyl-, -substituted cycloalkyl-, -oxy-,-alkoxy-, -substituted alkoxy-, -thio-, -amino-, or -substituted amino-.More particular still, L is single a covalent bond. Alternatively, L is-alkyl- or -substituted alkyl-; more particularly -pentyl- or-polyethylglycol- or -amino-dPEG₄-acid. Alternatively, L is -substitutedheterocyclyl-; more particularly, -piperidine-1-carbonyl-.

In another embodiment, R¹ and R² are chloro. In an alternative anotherembodiment R¹ and R² are fluoro.

In another embodiment, R³ is —COO⁻, —SO₃ ⁻, substituted azenyl, PEG,phosphate, or bisphosphonate. More particularly, R³ is —SO₃ ⁻.

In another embodiment, R^(a) is a dye. More particularly, the dye is axanthene, a cyanine, an indole, a benzofuran, a coumarin, or aborapolyazaindacine.

In another embodiment, R^(a) is a chelating moiety, a hapten, anantibody, an enzyme, a radiolabel, a metal ion or a particle comprisinga metal ion, a pigment, a chromogen, a phosphor, a fluorogen, abioluminescent substance, a chemiluminescent substance, or asemiconductor nanocrystal. More particularly, R^(a) is avidin,streptavidin or an analog thereof.

In another embodiment, the compound of Formula IA is a salt. Moreparticularly, the salt comprises a potassium or sodium ion.

In another embodiment, the reporter molecule is hydrophobic. In anotherembodiment, the compound of Formula IA is soluble in an aqueoussolution.

In another embodiment, the compound has a Formula IAA:

-   -   or a tautomer or stereoisomer thereof,    -   wherein,    -   R^(a) is a reporter molecule.

In another embodiment, the present compound has a Formula XXX

-   -   wherein the variables are as described herein, and each L group        is independent of the other.        Reporter Molecules

The reporter moelcules of the present invention functions as a reportermoiety to confer a detectable signal, directly or indirectly, to theconjugated carrier molecule, solid support or analyte, directly orindirectly, in a sample. This conjugated labeling reagent results in theability to detect, monitor, isolate, sequester, and quantitate a carriermolecule, a solid support or an analyte in a sample.

The present reporter molecules can be any reporter molecule known to oneskilled in the art. A wide variety of fluorescent dyes with appropriatereactivity may be suitable for incorporation into the compounds of theinvention are already known in the art (MOLECULAR PROBES HANDBOOK OFFLUORESCENT PROBES AND RESEARCH CHEMICALS by Richard P. Haugland,10^(th) Ed., (2005)). Reporter molecules include, without limitation, afluorophore, a fluorescent protein, a tandem dye (energy transfer pair),a ion chelating moiety, a radio label, spin labels, luminescent label,enzyme, hapten, colloid gold, quantum dot, nanocrystals, microspheres,or a fluorogenic enzyme substrate.

A fluorescent dye of the present invention is any chemical moiety thatexhibits an absorption maximum beyond 280 nm, and when covalently linkedto the ester moiety moiety of the present invention, forms a presentlabeling reagent.

Dyes of the present invention include, without limitation; a pyrene, ananthracene, a naphthalene, an acridine, a stilbene, an indole orbenzindole, an oxazole or benzoxazole, a thiazole or benzothiazole, a4-amino-7-nitrobenz-2-oxa-1,3-diazole (NBD), a carbocyanine (includingany corresponding compounds in U.S. Pat. Nos. 6,664,047; 6,977,305;6,974,873; 6,403,807; 6,348,599; 5,486,616; 5,268,486; 5,569,587;5,569,766; 5,627,027 and 6,048,982), a carbostyryl, a porphyrin, asalicylate, an anthranilate, an azulene, a perylene, a pyridine, aquinoline, a borapolyazaindacene (including any corresponding compoundsdisclosed in U.S. Pat. Nos. 4,774,339; 5,187,288; 5,248,782; 5,274,113;and 5,433,896), a xanthene (including any corresponding compoundsdisclosed in U.S. Pat. Nos. 6,162,931; 6,130,101; 6,229,055; 6,339,392;5,451,343 and 6,716,979), an oxazine or a benzoxazine, a carbazine(including any corresponding compounds disclosed in U.S. Pat. No.4,810,636), a phenalenone, a coumarin (including an correspondingcompounds disclosed in U.S. Pat. Nos. 5,696,157; 5,459,276; 5,501,980and 5,830,912), a benzofuran (including an corresponding compoundsdisclosed in U.S. Pat. Nos. 4,603,209 and 4,849,362) and benzphenalenone(including any corresponding compounds disclosed in U.S. Pat. No.4,812,409) and derivatives thereof. As used herein, oxazines includeresorufins (including any corresponding compounds disclosed in U.S. Pat.No. 5,242,805), aminooxazinones, diaminooxazines, and theirbenzo-substituted analogs.

Where the dye is a xanthene, the dye is optionally a fluorescein, arhodol (including any corresponding compounds disclosed in U.S. Pat.Nos. 5,227,487 and 5,442,045), a rosamine or a rhodamine (including anycorresponding compounds in U.S. Pat. Nos. 5,798,276; 5,846,737;5,847,162; 6,017,712; 6,025,505; 6,080,852; 6,716,979; 6,562,632). Asused herein, fluorescein includes benzo- or dibenzofluoresceins,seminaphthofluoresceins, or naphthofluoresceins. Similarly, as usedherein rhodol includes seminaphthorhodafluors (including anycorresponding compounds disclosed in U.S. Pat. No. 4,945,171).Fluorinated xanthene dyes have been described previously as possessingparticularly useful fluorescence properties (U.S. Pat. No. 6,162,931).

Preferred dyes of the invention include dansyl, xanthene, cyanine,borapolyazaindacene, pyrene, naphthalene, coumarin, oxazine andderivatives thereof. Preferred xanthenes are fluorescein, rhodamine andderivatives thereof, naphthalene and dansyl.

Typically the dye contains one or more aromatic or heteroaromatic rings,that are optionally substituted one or more times by a variety ofsubstituents, including without limitation, halogen, nitro, sulfo,cyano, alkyl, perfluoroalkyl, alkoxy, alkenyl, alkynyl, cycloalkyl,arylalkyl, acyl, aryl or heteroaryl ring system, benzo, or othersubstituents typically present on chromophores or fluorophores known inthe art.

In an exemplary embodiment, the dyes are independently substituted bysubstituents selected from the group consisting of hydrogen, halogen,amino, substituted amino, alkyl, substituted alkyl, aryl, substitutedaryl, heteroaryl, substituted heteroaryl, alkoxy, sulfo, reactive groupand carrier molecule. In another embodiment, the xanthene dyes of thisinvention comprise both compounds substituted and unsubstituted on thecarbon atom of the central ring of the xanthene by substituentstypically found in the xanthene-based dyes such as phenyl andsubstituted-phenyl moieties. Most preferred dyes are rhodamine,fluorescein, dansyl, naphthalene and derivatives thereof. The choice ofthe dye attached to the chelating moiety will determine the metalion-binding compound's absorption and fluorescence emission propertiesas well as its live cell properties, i.e. ability to localize tomitochondria.

Selected sulfonated reporter molecules also exhibit advantageousproperties, and include sulfonated pyrenes, coumarins, carbocyanines,and xanthenes (as described in U.S. Pat. Nos. 5,132,432; 5,696,157;5,268,486; 6,130,101). Sulfonated pyrenes and coumarins are typicallyexcited at wavelengths below about 450 nm (U.S. Pat. Nos. 5,132,432 and5,696,157).

Fluorescent proteins also find use as reporter moieties for the chelatecompounds of the present invention. Examples of fluorescent proteinsinclude green fluorescent protein (GFP) and the phycobiliproteins andthe derivatives thereof. The fluorescent proteins, especiallyphycobiliproteins, are particularly useful for creating tandemdye-reporter molecules. These tandem dyes comprise a fluorescent proteinand a fluorophore for the purposes of obtaining a larger Stokes shift,wherein the emission spectra are farther shifted from the wavelength ofthe fluorescent protein's absorption spectra. This property isparticularly advantageous for detecting a low quantity of a target ionin a sample wherein the emitted fluorescent light is maximallyoptimized; in other words, little to none of the emitted light isreabsorbed by the fluorescent protein. For this to work, the fluorescentprotein and fluorophore function as an energy transfer pair wherein thefluorescent protein emits at the wavelength that the acceptorfluorophore absorbs and the fluorophore then emits at a wavelengthfarther from the fluorescent proteins than could have been obtained withonly the fluorescent protein. Alternatively, the fluorophore functionsas the energy donor and the fluorescent protein is the energy acceptor.Particularly useful fluorescent proteins are the phycobiliproteinsdisclosed in U.S. Pat. Nos. 4,520,110; 4,859,582; 5,055,556 and thefluorophore bilin protein combinations disclosed in U.S. Pat. No.4,542,104. Alternatively, two or more fluorophore dyes can function asan energy transfer pair wherein one fluorophore is a donor dye and theother is the acceptor dye including any dye compounds disclosed in U.S.Pat. Nos. 6,358,684; 5,863,727; 6,372,445; 6,221,606; 6,008,379;5,945,526; 5,863,727; 5,800,996; 6,335,440; 6,008,373; 6,184,379;6,140,494 and 5,656,554.

The carrier molecules and solid supports may comprise a linker that isused to covalently attach the substituents to the present ester. Thesolid support or carrier molecule may be directly attached (where Linkeris a single bond) to the moieties or attached through a series of stablebonds. When the linker is a series of stable covalent bonds the linkertypically incorporates 1-30 nonhydrogen atoms selected from the groupconsisting of C, N, O, S and P. When the linker is not a single covalentbond, the linker may be any combination of stable chemical bonds,optionally including, single, double, triple or aromatic carbon-carbonbonds, as well as carbon-nitrogen bonds, nitrogen-nitrogen bonds,carbon-oxygen bonds, sulfur-sulfur bonds, carbon-sulfur bonds,phosphorus-oxygen bonds, phosphorus-nitrogen bonds, andnitrogen-platinum bonds. Typically the linker incorporates less than 15nonhydrogen atoms and are composed of any combination of ether,thioether, thiourea, amine, ester, carboxamide, sulfonamide, hydrazidebonds and aromatic or heteroaromatic bonds. Typically the linker is acombination of single carbon-carbon bonds and carboxamide, sulfonamideor thioether bonds. The bonds of the linker typically result in thefollowing moieties that can be found in the linker: ether, thioether,carboxamide, thiourea, sulfonamide, urea, urethane, hydrazine, alkyl,aryl, heteroaryl, alkoky, cycloalkyl and amine moieties. Examples of alinker include substituted or unsubstituted polymethylene, arylene,alkylarylene, arylenealkyl, or arylthio.

In one embodiment, the linker contains 1-6 carbon atoms; in another, thelinker comprises a thioether linkage. Exemplary linking members includea moiety that includes —C(O)NH—, —C(O)O—, —NH—, —S—, —O—, and the like.In another embodiment, the linker is or incorporates the formula—(CH₂)_(d)(CONH(CH₂)_(e))_(z)— or where d is an integer from 0-5, e isan integer from 1-5 and z is 0 or 1. In a further embodiment, the linkeris or incorporates the formula —O—(CH₂)—. In yet another embodiment, thelinker is or incorporates a phenylene or a 2-carboxy-substitutedphenylene.

Detection of the present labeling reagent is performed using methods andreagents well known to those skilled in the art. A preferred method ofdetection of the invention is through the use of fluorescence.Fluorescence from the complex can be visualized with a variety ofimaging techniques, including ordinary light or fluorescence microscopy,confocal laser-scanning microscopy, and flow cytometry, optionally usingimage deconvolution algorithms. Three-dimensional imaging resolutiontechniques in confocal microscopy utilize knowledge of the microscope'spoint spread function (image of a point source) to place out-of-focuslight in its proper perspective. Multiple-reporter molecule targetmaterials are optionally resolved spatially, chronologically, by size,or using detectably different spectral characteristics (includingexcitation and emission maxima, fluorescence intensity, fluorescencelifetime, fluorescence polarization, fluorescence photobleaching rates,or combinations thereof), or by combinations of these attributes.Typically, multiple-reporter molecule target materials are resolvedusing different labeling proteins with distinct spectral characteristicsfor each target material. Alternatively, the reporter molecules on thelabeling proteins are the same but the samples are reporter molecule andviewed sequentially or are spatially separated.

Additionally, enzymes can be used where there occurs an enzyme-dependentsecondary generation of signal, such as the formation of a coloredproduct from a non-colored substrate. Enzyme reporter molecules orenzyme labeling systems are desirable in that they can achieve signalamplification and greater distinctions from backgrounds. The enzymebreaks down a substrate to produce a chromophore or fluorophore or otherdetectable signal, thus amplifying the sensitivity of the assay and, ifthe substrate yields a distinct product at or near its site offormation, visualizing the site of the antigen/antibody complex in thesample. The substrate is selected to yield the preferred measurableproduct. Chromogenic, fluorogenic and chemiluminescence-generatingenzyme substrates are preferred. These enzymes are enzymes for whichsubstrates yielding useful chromophores, fluorophores, orchemiluminescence are known. Such substrates are extensively used in theart and are described the MOLECULAR PROBES HANDBOOK OF FLUORESCENTPROBES AND RESEARCH CHEMICALS by Richard P. Haugland, 10^(th) Ed.,(2005).

Preferred enzyme substrates of the invention are enzyme substrates thatyield a fluorescent product that localizes at or near the site of enzymeactivity. Enzymes of use in the method include any enzymes that utilizea chromogenic, fluorogenic, or chemiluminescence-generating substrate.Preferred enzymes of the invention include peroxidases, phosphatases,glycosidases, aequorins, or luciferases, and more specifically, HRP,Coprinus cinereus peroxidase, Arthromyces ramosus peroxidase, alkalinephosphatase, β-galactosidase, β-glucuronidase, or a protein A or proteinG fusion protein of luciferase.

A preferred chromogenic (and in some cases fluorogenic) substrate andenzyme combination uses oxidoreductases such as horseradish peroxidase,Coprinus cinereus peroxidase, or Arthromyces ramosus peroxidase and asubstrate such as 3,3′-diaminobenzidine (DAB) or3-amino-9-ethylcarbazole (AEC), which yield a distinguishing color(brown and red, respectively). Other chromogenic oxidoreductasesubstrates that yield detectable products include, but are not limitedto: 2,2′-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid (ABTS),o-phenylenediamine (OPD), 3,3′,5,5′-tetramethylbenzidine (TMB),o-dianisidine, 5-aminosalicylic acid, and 4-chloro-1-naphthol.Fluorogenic substrates include, but are not limited to, homovanillicacid or 4-hydroxy-3-methoxyphenylacetic acid, reduced phenoxazines andreduced benzothiazines, including the Amplex Red reagent and itsvariants (Miike, U.S. Pat. No. 4,384,042), reduced dihydroxanthenes,including the Amplex Gold reagent and other dihydrofluoresceins such asthose described in U.S. Pat. No. 6,162,931, and dihydrorhodamines suchas dihydrorhodamine 123. Peroxidase substrates that are tyramides, asdescribed in U.S. Pat. Nos. 5,196,306; 5,583,001 and 5,731,158, whichare incorporated by reference, represent a unique class of peroxidasesubstrates in that they can be intrinsically detectable before action ofthe enzyme but are “fixed in place” by the action of a peroxidase in theprocess termed tyramide signal amplification (TSA). These substrates,which are a preferred embodiment of the instant invention, areextensively utilized to reporter molecule targets in samples that arecells, tissues, or arrays for their subsequent detection by microscopy,flow cytometry, optical scanning, and fluorometry.

Another preferred chromogenic (and in some cases fluorogenic) substrateand enzyme combination uses a phosphatase enzyme such as calf intestinalalkaline phosphatase, an acid phosphatase, or a recombinant version ofsuch a phosphatase in combination with a chromogenic substrate such as5-bromo-4-chloro-3-indolyl phosphate (BCIP), 6-chloro-3-indolylphosphate, 5-bromo-6-chloro-3-indolyl phosphate, p-nitrophenylphosphate, or o-nitrophenyl phosphate or with a fluorogenic substratesuch as 4-methylumbelliferyl phosphate, carboxyumbelliferyl phosphate,6,8-difluoro-7-hydroxy-4-methylcoumarinyl phosphate (DiFMUP, U.S. Pat.No. 5,830,912), fluorescein diphosphate, 3-O-methylfluoresceinphosphate, resorufin phosphate,9H-(1,3-dichloro-9,9-dimethylacridin-2-one-7-yl) phosphate (DDAOphosphate), or ELF 97, ELF 39, or related phosphates (U.S. Pat. Nos.5,316,906 and 5,443,986).

Glycosidases, in particularly β-galactosidase, β-glucuronidase, andβ-glucosidase, are additional suitable enzymes. Appropriate chromogenicsubstrates include, but are not limited to, 5-bromo-4-chloro-3-indolylβ-D-galactopyranoside (X-gal) and similar indolyl galactosides,glucosides, and glucuronides, o-nitrophenyl β-D-galactopyranoside(ONPG), and p-nitrophenyl β-D-galactopyranoside. Preferred fluorogenicglycosidase substrates include resorufin β-D-galactopyranoside,fluorescein digalactoside (FDG), fluorescein diglucuronide and theirstructural variants (U.S. Pat. Nos. 5,208,148; 5,242,805; 5,362,628;5,576,424 and 5,773,236), 4-methylumbelliferyl β-D-galactopyranoside,carboxyumbelliferyl β-D-galactopyranoside, and fluorinated coumarinβ-D-galactopyranosides (U.S. Pat. No. 5,830,912).

Additional enzymes include, but are not limited to, hydrolases such ascholinesterases and peptidases, oxidases such as glucose oxidase andcytochrome oxidases, and reductases, for which suitable substrates areknown.

When using florescent dyes to detect the desired target the sample isilluminated at a suitable absorption wavelength. A suitable wavelengthis one that comes within the range of absorption wavelengths for each ofthe fluorescent dyes being used. Typically, the mixture is illuminatedby a light source capable of producing light at or near the wavelengthof maximum absorption of the dye or dyes, such as by ultraviolet orvisible lamp, an arc lamp, a laser, or even sunlight. Illumination ofthe sample at a suitable wavelength results in one or more illuminatedtargets that are then analyzed according to the response of theirfluorescence to the illumination. The illuminated targets are observedwith any of a number of means for detecting a fluorescent responseemitted from the illuminated target, including but not limited to visualinspection, cameras and film or other imaging equipment, or use ofinstrumentation such as fluorometers, plate readers, laser-basedscanners, microscopes, or flow cytometers, or by means for amplifyingthe signal such as a photomultiplier (PMT).

-   -   In another embodiment, R^(a) is:

-   -   or a tautomer or salt thereof;    -   wherein,    -   R⁴, R⁵, R⁶, R⁷, and R⁸ are each independently selected from the        group consisting of H, alkyl, substituted alkyl, alkoxy,        substituted alkoxy, acyl, acylamino, acyloxy, amino, substituted        amino, aminocarbonyl, aminothiocarbonyl, aminocarbonylamino,        aminothiocarbonylamino, aminocarbonyloxy, aminosulfonyl,        aminosulfonyloxy, aminosulfonylamino, amidino, carboxyl,        carboxyl ester, (carboxyl ester)amino, (carboxyl ester)oxy,        cyano, halo, hydroxy, nitro, SO₃—, sulfonyl, substituted        sulfonyl, sulfonyloxy, thioacyl, thiol, alkylthio, substituted        alkylthio, aryl, substituted aryl, heteroaryl, substituted        heteroaryl, cycloalkyl, substituted cycloalkyl, heterocyclyl,        and substituted heterocyclyl; or one or both of R⁴ and R⁷ and R⁸        and R⁶ are taken together to form a fused aryl or heteroaryl        group; and    -   one of R⁴, R⁵, R⁶, R⁷, and R⁸ is the point of attachment to L        through a covalent bond, -alkyl-, -substituted alkyl-,        -alkenyl-, -substituted alkenyl-, -heterocyclyl-, -substituted        heterocyclyl-, -aryl-, -substituted aryl-, -heteroaryl-,        -substituted heteroaryl-, -cycloakyl-, -substituted cycloalkyl-,        -oxy-, -alkoxy-, -substituted alkoxy-, -thio-, -amino-, or        -substituted amino-.

More particularly, R⁴ and R⁵ are amino or imino. More particular still,R⁶ and R⁷ are H. In another embodiment R³ is the point of attachment toL through a phenyl. More particularly, the phenyl is substituted with acarboxyl group. In a more particular embodiment thereof, R^(a) isappended to L at the para or meta position, with respect to the xanthenemoiety.

-   -   In a more particular embodiment thereof, R^(a) has the following        structure:

-   -   wherein the R groups are defined herein.    -   In another embodiment, R^(a) is:

-   -   or a tautomer or salt thereof;    -   wherein,    -   Z¹ and Z² are each independently O, S, NR¹⁷ or CR¹⁸R¹⁹;    -   Y is —CR¹⁴═(CR¹⁵—CR¹⁶═)_(m);    -   m is 0, 1, 2, or 3;    -   R¹⁰ and R¹¹ are each independently selected from the group        consisting of H, alkyl, substituted alkyl, alkoxy, substituted        alkoxy, acyl, acylamino, acyloxy, amino, substituted amino,        aminocarbonyl, aminothiocarbonyl, aminocarbonylamino,        aminothiocarbonylamino, aminocarbonyloxy, aminosulfonyl,        aminosulfonyloxy, aminosulfonylamino, amidino, carboxyl,        carboxyl ester, (carboxyl ester)amino, (carboxyl ester)oxy,        cyano, halo, hydroxy, nitro, SO₃ ⁻, sulfonyl, substituted        sulfonyl, sulfonyloxy, thioacyl, thiol, alkylthio, substituted        alkylthio, aryl, substituted aryl, heteroaryl, substituted        heteroaryl, cycloalkyl, substituted cycloalkyl, heterocyclyl,        and substituted heterocyclyl;    -   R¹², R¹³ and R¹⁷ are each independently H, alkyl, substituted        alkyl, cycloalkyl, substituted cycloalkyl, aryl, substituted        aryl, heteroaryl, substituted heteroaryl, heterocyclyl,        substituted heterocyclyl; and    -   R¹⁴, R¹⁵ and R¹⁶ are each independently, H, alkyl, substituted        alkyl, cycloalkyl, substituted cycloalkyl, aryl, substituted        aryl, heteroaryl, or substituted heteroaryl;    -   R¹⁸ and R¹⁹ are H, alkyl or substituted alkyl;    -   wherein one of R¹⁰, R¹¹, R¹², R¹³, R¹⁴, R¹⁵, R¹⁶, R¹⁷, R¹⁸ and        R¹⁹ is the point of attachment to L through a covalent bond,        -alkyl-, -substituted alkyl-, -alkenyl-, -substituted alkenyl-,        -heterocyclyl-, -substituted heterocyclyl-, -aryl-, -substituted        aryl-, -heteroaryl-, -substituted heteroaryl-, -cycloakyl-,        -substituted cycloalkyl-, -oxy-, -alkoxy-, -substituted alkoxy-,        -thio-, -amino-, or -substituted amino-.    -   In another more particular embodiment, Z¹ and Z² are both        CR¹⁸R¹⁹. More particular still, R¹⁸ and R¹⁹ are both methyl.        Alternatively, in a preferred embodiment R¹⁹ is methyl and R¹⁸        is the point of attachment to L through an -alkyl- or        -substituted alkyl-. In another alternate embodiment, R¹⁸ and        R¹⁹ are both methyl and the point of attachment to L is through        an -alkyl- or -substituted alkyl- at R¹³. More particular still,        at least one or both of R¹² and R¹³ are propanylsulfonate.    -   In another more particular embodiment, R^(a) is:

-   -   or a tautomer or salt thereof;    -   wherein,    -   R²⁰, R²¹, R²², R²³, R²⁴ and R²⁵ are each independently selected        from the group consisting of H, alkyl, substituted alkyl,        alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino,        substituted amino, aminocarbonyl, aminothiocarbonyl,        aminocarbonylamino, aminothiocarbonylamino, aminocarbonyloxy,        aminosulfonyl, aminosulfonyloxy, aminosulfonylamino, amidino,        carboxyl, carboxyl ester, (carboxyl ester)amino, (carboxyl        ester)oxy, cyano, halo, hydroxy, nitro, SO₃—, sulfonyl,        substituted sulfonyl, sulfonyloxy, thioacyl, thiol, alkylthio,        substituted alkylthio, aryl, substituted aryl, heteroaryl,        substituted heteroaryl, cycloalkyl, substituted cycloalkyl,        heterocyclyl, and substituted heterocyclyl; and    -   one of R²⁰, R²¹, R²², R²³, R²⁴ and R²⁵ is the point of        attachment to L through a covalent bond, -alkyl-, -substituted        alkyl-, -alkenyl-, -substituted alkenyl-, -heterocyclyl-,        -substituted heterocyclyl-, -aryl-, -substituted aryl-,        -heteroaryl-, -substituted heteroaryl-, -cycloakyl-,        -substituted cycloalkyl-, -oxy-, -alkoxy-, -substituted alkoxy-,        -thio-, -amino-, or -substituted amino-.    -   In another more particular embodiment, R^(a) is:

-   -   or a tautomer or salt thereof;    -   wherein,    -   R³⁰, R³¹, R³², R³³, R³⁴, R³⁵ and R³⁶ are each independently        selected from the group consisting of H, alkyl, substituted        alkyl, alkoxy, substituted alkoxy, acyl, acylamino, acyloxy,        amino, substituted amino, aminocarbonyl, aminothiocarbonyl,        aminocarbonylamino, aminothiocarbonylamino, aminocarbonyloxy,        aminosulfonyl, aminosulfonyloxy, aminosulfonylamino, amidino,        carboxyl, carboxyl ester, (carboxyl ester)amino, (carboxyl        ester)oxy, cyano, halo, hydroxy, nitro, SO₃—, sulfonyl,        substituted sulfonyl, sulfonyloxy, thioacyl, thiol, alkylthio,        substituted alkylthio, aryl, substituted aryl, heteroaryl,        substituted heteroaryl, cycloalkyl, substituted cycloalkyl,        heterocyclyl, and substituted heterocyclyl; and    -   one of R³⁰, R³¹, R³², R³³, R³⁴, R³⁵ and R³⁶ is the point of        attachment to L through a covalent bond, -alkyl-, -substituted        alkyl-, -alkenyl-, -substituted alkenyl-, -heterocyclyl-,        -substituted heterocyclyl-, -aryl-, -substituted aryl-,        -heteroaryl-, -substituted heteroaryl-, -cycloakyl-,        -substituted cycloalkyl-, -oxy-, -alkoxy-, -substituted alkoxy-,        -thio-, -amino-, or -substituted amino-.    -   In another more particular embodiment, R^(a) is:

-   -   or a tautomer or salt thereof;    -   wherein,    -   R⁴⁰, R⁴¹, R⁴², R⁴³, R⁴⁴ and R⁴⁵ are each independently selected        from the group consisting of H, alkyl, substituted alkyl,        alkoxy, substituted alkoxy, acyl, acylamino, acyloxy, amino,        substituted amino, aminocarbonyl, aminothiocarbonyl,        aminocarbonylamino, aminothiocarbonylamino, aminocarbonyloxy,        aminosulfonyl, aminosulfonyloxy, aminosulfonylamino, amidino,        carboxyl, carboxyl ester, (carboxyl ester)amino, (carboxyl        ester)oxy, cyano, halo, hydroxy, nitro, SO₃—, sulfonyl,        substituted sulfonyl, sulfonyloxy, thioacyl, thiol, alkylthio,        substituted alkylthio, aryl, substituted aryl, heteroaryl,        substituted heteroaryl, cycloalkyl, substituted cycloalkyl,        heterocyclyl, and substituted heterocyclyl; and    -   one of R⁴⁰, R⁴¹, R⁴², R⁴³, R⁴⁴ and R⁴⁵ is the point of        attachment to L through a covalent bond, -alkyl-, -substituted        alkyl-, -alkenyl-, -substituted alkenyl-, -heterocyclyl-,        -substituted heterocyclyl-, -aryl-, -substituted aryl-,        -heteroaryl-, -substituted heteroaryl-, -cycloakyl-,        -substituted cycloalkyl-, -oxy-, -alkoxy-, -substituted alkoxy-,        -thio-, -amino-, or -substituted amino-.    -   Another aspect of the invention provides a compound of Formula        II or a tautomer or salt thereof:

-   -   wherein,    -   L is a linker;    -   R¹ is a halogen;    -   R² is a halogen;    -   R³ is a water solubilizing group;    -   R⁶, R⁷ and R⁹ are each independently selected from the group        consisting of H, alkyl, substituted alkyl, alkoxy, substituted        alkoxy, acyl, acylamino, acyloxy, amino, substituted amino,        aminocarbonyl, aminothiocarbonyl, aminocarbonylamino,        aminothiocarbonylamino, aminocarbonyloxy, aminosulfonyl,        aminosulfonyloxy, aminosulfonylamino, amidino, carboxyl,        carboxyl ester, (carboxyl ester)amino, (carboxyl ester)oxy,        cyano, halo, hydroxy, nitro, SO₃—, sulfonyl, substituted        sulfonyl, sulfonyloxy, thioacyl, thiol, alkylthio, substituted        alkylthio, aryl, substituted aryl, heteroaryl, substituted        heteroaryl, cycloalkyl, substituted cycloalkyl, heterocyclyl,        and substituted heterocyclyl; and    -   n is 0, 1, or 2.

More particularly, R⁶ and R⁷ are H. In another embodiment R⁹ is acarboxyl group.

In another more particular embodiment, L is a covalent bond, -alkyl-,-substituted alkyl-, -alkenyl-, -substituted alkenyl-, -heterocyclyl-,-substituted heterocyclyl-, -aryl-, -substituted aryl-, -heteroaryl-,-substituted heteroaryl-, -cycloakyl-, -substituted cycloalkyl-, -oxy-,-alkoxy-, -substituted alkoxy-, -thio-, -amino-, or -substituted amino-.

In another embodiment, R¹ and R² are chloro.

-   -   -   In another embodiment, R³ is —COO⁻, —SO₃ ⁻, substituted            azenyl, PEG, phosphate, or bisphosphonate. More            particularly, R³ is —SO₃ ⁻.        -   In another embodiment, the compound of Formula II is a salt.            More particularly, the salt comprises a potassium or sodium            ion. In another embodiment, the compound of Formula II is            soluble in an aqueous solution.        -   Another aspect of the invention provides a compound of            Formula III or a tautomer or salt thereof:

-   -   wherein,    -   Y is —CR¹⁴═(CR¹⁵—CR¹⁶═)_(m);    -   m is 0, 1, 2, or 3;    -   R¹⁰ and R¹¹ are each independently selected from the group        consisting of H, alkyl, substituted alkyl, alkoxy, substituted        alkoxy, acyl, acylamino, acyloxy, amino, substituted amino,        aminocarbonyl, aminothiocarbonyl, aminocarbonylamino,        aminothiocarbonylamino, aminocarbonyloxy, aminosulfonyl,        aminosulfonyloxy, aminosulfonylamino, amidino, carboxyl,        carboxyl ester, (carboxyl ester)amino, (carboxyl ester)oxy,        cyano, halo, hydroxy, nitro, SO₃—, sulfonyl, substituted        sulfonyl, sulfonyloxy, thioacyl, thiol, alkylthio, substituted        alkylthio, aryl, substituted aryl, heteroaryl, substituted        heteroaryl, cycloalkyl, substituted cycloalkyl, heterocyclyl,        and substituted heterocyclyl;    -   R¹² and R¹³ are each independently H, alkyl, substituted alkyl,        cycloalkyl, substituted cycloalkyl, aryl, substituted aryl,        heteroaryl, substituted heteroaryl, heterocyclyl, substituted        heterocyclyl;    -   R¹⁸ is methyl; and    -   wherein one of R¹³ or R¹⁸ is:

-   -   L is a linker;    -   R¹ is a halogen;    -   R² is a halogen; and    -   R³ is a water solubilizing group.

More particularly, R¹ and R² are chloro. More particular still, R³ is—SO₃ ⁻. More particular still, R¹⁸ and R¹⁹ are both methyl. In apreferred embodiment R¹⁹ is methyl and R¹⁸ is the point of attachment toL through an -alkyl- or -substituted alkyl-. In another alternateembodiment, R¹⁸ and R¹⁹ are both methyl and the point of attachment to Lis through an -alkyl- or -substituted alkyl- at R¹³.

In another more particular embodiment, L is a covalent bond, -alkyl-,-substituted alkyl-, -alkenyl-, -substituted alkenyl-, -heterocyclyl-,-substituted heterocyclyl-, -aryl-, -substituted aryl-, -heteroaryl-,-substituted heteroaryl-, -cycloakyl-, -substituted cycloalkyl-, -oxy-,-alkoxy-, -substituted alkoxy-, -thio-, -amino-, or -substituted amino-.

In another more particular embodiment, R^(a) is:

-   -   wherein the R-groups are defined herein.

Another aspect of the invention provides a compound selected from thegroup consisting of:

Another aspect of the invention provides a compound having the followingstructure or a tautomer or salt thereof:

-   -   wherein,    -   R¹ is a halogen;    -   R² is a halogen; and    -   R³ is a water solubilizing group.

In another embodiment, R¹ and R² are chloro. More particularly, R³ is—SO₃ ⁻.

In a preferred embodiment, any one of the aforementioned compounds isused in the methods described below.

Preparation of Conjugates

In another embodiment is provided a method for forming conjugates of thepresent reporter molecules and a carrier molecule or solid support. Thismethod comprises:

-   -   a) combining a reporter molecule with a carrier molecule or        solid support to form a combined sample, wherein the compound        comprises a reactive group as described herein, such as the        compound of Formula IA; and,    -   b) incubating the combined sample for a sufficient amount of        time for the compound to form a covalent bond with either the        carrier molecule or solid support whereby a conjugate is formed.

The conjugates of the carrier molecules or solid supports, e.g., drugs,peptides, toxins, nucleotides, phospholipids and other organic moleculesare prepared by organic synthesis methods using the reactive dyes of theinvention and are generally prepared by means well recognized in the art(Haugland, MOLECULAR PROBES, supra, (2005)). Preferably, conjugation toform a covalent bond consists of simply mixing the reactive compounds ofthe present invention in a suitable solvent in which both the reactivecompound and the substance to be conjugated are soluble. The reactionpreferably proceeds spontaneously without additional reagents at roomtemperature or below. Chemical modification of water-insolublesubstances, so that a desired compound-conjugate may be prepared, ispreferably performed in an aprotic solvent such as dimethylformamide,dimethylsulfoxide, acetone, ethyl acetate, toluene, or chloroform.Similar modification of water-soluble materials is readily accomplishedthrough the use of the compounds of the present invention to make themmore readily soluble in organic solvents.

Preparation of peptide or protein conjugates typically comprises firstdissolving the protein to be conjugated in aqueous buffer at about0.1-10 mg/mL at room temperature or below. Bicarbonate buffers (pH about8.3) are especially suitable for reaction with succinimidyl esters,phosphate buffers (pH about 7.2-8) for reaction with thiol-reactivefunctional groups and carbonate or borate buffers (pH about 9) forreaction with isothiocyanates and dichlorotriazines. The appropriatereactive compound is then dissolved in a nonhydroxylic solvent (usuallyDMSO or DMF) in an amount sufficient to give a suitable degree ofconjugation when added to a solution of the protein to be conjugated.The appropriate amount of compound for any protein or other component isconveniently predetermined by experimentation in which variable amountsof the compound are added to the protein, the conjugate ischromatographically purified to separate unconjugated compound and thecompound-protein conjugate is tested in its desired application.

Following addition of the reactive compound to the component solution,the mixture is incubated for a suitable period (typically about 1 hourat room temperature to several hours on ice), the excess compound isremoved by gel filtration, dialysis, HPLC, adsorption on an ion exchangeor hydrophobic polymer or other suitable means. The compound-conjugateis used in solution or lyophilized. In this way, suitable conjugates canbe prepared from antibodies, antibody fragments, avidins, lectins,enzymes, proteins A and G, cellular proteins, albumins, histones, growthfactors, hormones, and other proteins.

Conjugates of polymers, including biopolymers and other higher molecularweight polymers are typically prepared by means well recognized in theart (for example, Brinkley et al., Bioconjugate Chem., 3: 2 (1992)). Inthese embodiments, a single type of reactive site may be available, asis typical for polysaccharides) or multiple types of reactive sites(e.g. amines, thiols, alcohols, phenols) may be available, as is typicalfor proteins. Selectivity of labeling is best obtained by selection ofan appropriate reactive dye. For example, modification of thiols with athiol-selective reagent such as a haloacetamide or maleimide, ormodification of amines with an amine-reactive reagent such as anactivated ester, acyl azide, isothiocyanate or3,5-dichloro-2,4,6-triazine. Partial selectivity can also be obtained bycareful control of the reaction conditions.

When modifying polymers with the compounds, an excess of compound istypically used, relative to the expected degree of compoundsubstitution. Any residual, unreacted compound or a compound hydrolysisproduct is typically removed by dialysis, chromatography orprecipitation. Presence of residual, unconjugated dye can be detected bythin layer chromatography using a solvent that elutes the dye away fromits conjugate. In all cases it is usually preferred that the reagents bekept as concentrated as practical so as to obtain adequate rates ofconjugation.

In an exemplary embodiment, the conjugate of the invention is associatedwith an additional substance, that binds either to the fluorophore orthe conjugated substance (carrier molecule or solid support) throughnoncovalent interaction. In another exemplary embodiment, the additionalsubstance is an antibody, an enzyme, a hapten, a lectin, a receptor, anoligonucleotide, a nucleic acid, a liposome, or a polymer. Theadditional substance is optionally used to probe for the location of theconjugate, for example, as a means of enhancing the signal of theconjugate.

Another aspect of the invention provides a method of making a compoundof Formula I comprising:

-   -   contacting a carrier molecule or a solid support comprising a        nucleophile with a compound of Formula IA or a tautomer or salt        thereof:

-   -   wherein,    -   L is a linker;    -   R¹ is a halogen;    -   R² is a halogen;    -   R³ comprises a water solubilizing group; and    -   R^(a) is a reporter molecule;    -   forming a compound of Formula I or a tautomer or salt thereof:

-   -   wherein,    -   L is the linker;    -   R^(a) is the reporter molecule; and    -   R^(b) is the carrier molecule or solid support comprising a        nucleophile (X).

In another more particular embodiment, L is a covalent bond, -alkyl-,-substituted alkyl-, -alkenyl-, -substituted alkenyl-, -heterocyclyl-,-substituted heterocyclyl-, -aryl-, -substituted aryl-, -heteroaryl-,-substituted heteroaryl-, -cycloakyl-, -substituted cycloalkyl-, -oxy-,-alkoxy-, -substituted alkoxy-, -thio-, -amino-, or -substituted amino-.

In another embodiment, R¹ and R² are chloro.

In another embodiment, R³ is —COO⁻, —SO₃ ⁻, substituted azenyl, PEG,phosphate, or bisphosphonate. More particularly, R³ is —SO₃ ⁻.

In another embodiment, R^(a) is a dye. More particularly, the dye is axanthene, a cyanine, an indole, a benzofuran, a coumarin, or aborapolyazaindacine.

In another embodiment, R^(a) is a chelating moiety, a hapten, anantibody, an enzyme, a radiolabled, a metal ion or metal ion containingsubstance, a pigment, a chromogen, a phosphor, a fluorogen, abioluminescent substance, a chemiluminescent substance, or asemiconductor nanocrystal. More particularly, R^(a) is avidin,streptavidin or an analog thereof.

In another embodiment, the compound of Formula IA is a salt. Moreparticularly, the salt comprises a potassium or sodium ion.

In another embodiment, the reporter molecule is hydrophobic. In anotherembodiment, the compound of Formula IA is soluble in an aqueoussolution. Accordingly, the SDP ester solubilizes hydrophobic reportermolecules in aqueous solution, thereby permitting reaction withhydrophilic carrier molecules and supports in aqueous solutions, whereorganic solvents may lead to disruption or denaturing of the nativestructure of the molecules.

In another embodiment, R^(b) is a solid support. More particularly,R^(b) is a column or gel. Alternatively, R^(b) is a carrier molecule.More particular still, the carrier molecule is selected from the groupconsisting of an amino acid, a peptide, a protein, a carbohydrate, apolysaccharide, a nucleoside, a nucleotide, an oligonucleotide, anucleic acid polymer, a drug, a lipid, and a synthetic polymer. Moreparticularly, the carrier molecule is a protein.

Another embodiment of the invention, further comprises incubating thecarrier molecule or solid support with the compound of Formula IA afterthe contacting step.

In another embodiment, the contacting step is done in an aqueoussolution.

In another embodiment, X is an amino, thio, or oxo group.

Another aspect of the invention provides a method of labeling a carriermolecule or solid support comprising:

-   -   contacting the carrier molecule or solid support with a compound        of Formula IA or a tautomer or salt thereof:

-   -   wherein,    -   L is a linker;    -   R¹ is a halogen;    -   R² is a halogen;    -   R³ comprises a water solubilizing group;    -   R^(a) is a reporter molecule; and    -   the carrier molecule or solid support comprises a nucleophile;        and    -   forming a reporter molecule carrier molecule or solid support.

In a more particular embodiment, the labeled carrier molecule or solidsupport comprises a compound of Formula I:

-   -   wherein,    -   R^(a) is the reporter molecule; and    -   R^(b) is the carrier molecule or solid support comprising a        nucleophile (x).

Another aspect of the invention provides a method of making a compoundof Formula IA or a tautomer or salt thereof comprising:

-   -   contacting a compound of Formula IB or a tautomer or salt        thereof:

-   -   with a compound of Formula IC or a tautomer or salt thereof:

-   -   and forming the compound of Formula IA or a tautomer or salt        thereof:

-   -   wherein,    -   R¹ is a halogen;    -   R² is a halogen;    -   R³ comprises a water solubilizing group;    -   L is a linker; and    -   R^(a) is a reporter molecule.

In a more particular embodiment, the contacting step is done in thepresence of dimethylaminopyridine (DMAP). In another embodiment, thecontacting step is done in an organic solvent.

In general, compounds of the invention are generally prepared bycondensation of a phenol of the formula:

With a reporter molecule contain a carboxylic acid in organic oraqueous/organic solvent systems. The carboxylic acid can be activated insitu with a reagent such as a carbodiimide, followed by reaction withthe phenol XI. The carboxylic acid can also be activated by conversionto an electrophilic equivalent such as an acid chloride, followed byreaction with the phenol XI.

Alternatively, the phenol XI can be activated by conversion into auranium salt, either preparatively or in situ, followed by reaction witha carboxylic acid; this reaction can be facilitated by a catalyst suchas 4-dimethylaminopyridine (DMAP).

Carrier Molecules

A variety of carrier molecules are useful in the present invention.Exemplary carrier molecules include antigens, steroids, vitamins, drugs,haptens, metabolites, toxins, environmental pollutants, amino acids,peptides, proteins, nucleic acids, nucleic acid polymers, carbohydrates,lipids, and polymers.

In an exemplary embodiment, the carrier molecule comprises an aminoacid, a peptide, a protein, a polysaccharide, a nucleoside, anucleotide, an oligonucleotide, a nucleic acid, a hapten, a psoralen, adrug, a hormone, a lipid, a lipid assembly, a synthetic polymer, apolymeric microparticle, a biological cell, a virus and combinationsthereof. In another exemplary embodiment, the carrier molecule isselected from a hapten, a nucleotide, an oligonucleotide, a nucleic acidpolymer, a protein, a peptide or a polysaccharide. In another exemplaryembodiment, at least one R-group member (such as one of R¹-R⁴⁵) comprisea carrier molecule. In another exemplary embodiment one of the R-groupmembers comprises a solid support.

In an exemplary embodiment, the carrier molecule comprises an aminoacid, a peptide, a protein, a polysaccharide, a nucleoside, anucleotide, an oligonucleotide, a nucleic acid, a hapten, a psoralen, adrug, a hormone, a lipid, a lipid assembly, a synthetic polymer, apolymeric microparticle, a biological cell, a virus and combinationsthereof. In another exemplary embodiment, the carrier molecule isselected from a hapten, a nucleotide, an oligonucleotide, a nucleic acidpolymer, a protein, a peptide or a polysaccharide. In a preferredembodiment the carrier molecule is amino acid, a peptide, a protein, apolysaccharide, a nucleoside, a nucleotide, an oligonucleotide, anucleic acid, a hapten, a psoralen, a drug, a hormone, a lipid, a lipidassembly, a tyramine, a synthetic polymer, a polymeric microparticle, abiological cell, cellular components, an ion chelating moiety, anenzymatic substrate or a virus. In another preferred embodiment, thecarrier molecule is an antibody or fragment thereof, an antigen, anavidin or streptavidin, a biotin, a dextran, an antibody bindingprotein, a fluorescent protein, agarose, and a non-biologicalmicroparticle. Typically, the carrier molecule is an antibody, anantibody fragment, antibody-binding proteins, avidin, streptavidin, atoxin, a lectin, or a growth factor. Preferred haptens include biotin,digoxigenin and fluorophores.

Antibody binging proteins include, but are not limited to, protein A,protein G, soluble Fc receptor, protein L, lectins, anti-IgG, anti-IgA,anti-IgM, anti-IgD, anti-IgE or a fragment thereof.

In an exemplary embodiment, the enzymatic substrate is selected from anamino acid, peptide, sugar, alcohol, alkanoic acid, 4-guanidinobenzoicacid, nucleic acid, lipid, sulfate, phosphate, —CH₂OCOalkyl andcombinations thereof. Thus, the enzyme substrates can be cleave byenzymes selected from the group consisting of peptidase, phosphatase,glycosidase, dealkylase, esterase, guanidinobenzotase, sulfatase,lipase, peroxidase, histone deacetylase, endoglycoceramidase,exonuclease, reductase and endonuclease.

In another exemplary embodiment, the carrier molecule is an amino acid(including those that are protected or are substituted by phosphates,carbohydrates, or C₁ to C₂₂ carboxylic acids), or a polymer of aminoacids such as a peptide or protein. In a related embodiment, the carriermolecule contains at least five amino acids, more preferably 5 to 36amino acids. Exemplary peptides include, but are not limited to,neuropeptides, cytokines, toxins, protease substrates, and proteinkinase substrates. Other exemplary peptides may function as organellelocalization peptides, that is, peptides that serve to target theconjugated compound for localization within a particular cellularsubstructure by cellular transport mechanisms. Preferred protein carriermolecules include enzymes, antibodies, lectins, glycoproteins, histones,albumins, lipoproteins, avidin, streptavidin, protein A, protein G,phycobiliproteins and other fluorescent proteins, hormones, toxins andgrowth factors. Typically, the protein carrier molecule is an antibody,an antibody fragment, avidin, streptavidin, a toxin, a lectin, or agrowth factor. Exemplary haptens include biotin, digoxigenin andfluorophores.

In another exemplary embodiment, the carrier molecule comprises anucleic acid base, nucleoside, nucleotide or a nucleic acid polymer,optionally containing an additional linker or spacer for attachment of afluorophore or other ligand, such as an alkynyl linkage (U.S. Pat. No.5,047,519), an aminoallyl linkage (U.S. Pat. No. 4,711,955) or otherlinkage. In another exemplary embodiment, the nucleotide carriermolecule is a nucleoside or a deoxynucleoside or a dideoxynucleoside.

Exemplary nucleic acid polymer carrier molecules are single- ormulti-stranded, natural or synthetic DNA or RNA oligonucleotides, orDNA/RNA hybrids, or incorporating an unusual linker such as morpholinederivatized phosphates (AntiVirals, Inc., Corvallis Oreg.), or peptidenucleic acids such as N-(2-aminoethyl)glycine units, where the nucleicacid contains fewer than 50 nucleotides, more typically fewer than 25nucleotides.

In another exemplary embodiment, the carrier molecule comprises acarbohydrate or polyol that is typically a polysaccharide, such asdextran, FICOLL, heparin, glycogen, amylopectin, mannan, inulin, starch,agarose and cellulose, or is a polymer such as a poly(ethylene glycol).In a related embodiment, the polysaccharide carrier molecule includesdextran, agarose or FICOLL.

In another exemplary embodiment, the carrier molecule comprises a lipid(typically having 6-25 carbons), including glycolipids, phospholipids,and sphingolipids. Alternatively, the carrier molecule comprises a lipidvesicle, such as a liposome, or is a lipoprotein (see below). Somelipophilic substituents are useful for facilitating transport of theconjugated dye into cells or cellular organelles.

Alternatively, the carrier molecule is cells, cellular systems, cellularfragments, or subcellular particles. Examples of this type of conjugatedmaterial include virus particles, bacterial particles, virus components,biological cells (such as animal cells, plant cells, bacteria, oryeast), or cellular components. Examples of cellular components that canbe labeled, or whose constituent molecules can be labeled, include butare not limited to lysosomes, endosomes, cytoplasm, nuclei, histones,mitochondria, Golgi apparatus, endoplasmic reticulum and vacuoles.

In another embodiment the carrier molecule is a metal chelating moiety.While any chelator that binds a metal ion of interest and gives a changein its fluorescence properties is a suitable conjugate, preferred metalchelating moieties are crown ethers, including diaryldiaza crown ethers,as described in U.S. Pat. No. 5,405,975 to Kuhn et al. (1995);derivatives of 1,2-bis-(2-aminophenoxyethane)-N,N,N′,N′-tetraacetic acid(BAPTA), as described in U.S. Pat. No. 5,453,517 to Kuhn et al. (1995)(incorporated by reference) and U.S. Pat. No. 5,049,673 to Tsien et al.(1991); derivatives of 2-carboxymethoxy-aniline-N,N-diacetic acid(APTRA), as described by Ragu et al., Am. J. Physiol., 256: C540 (1989);and pyridyl-based and phenanthroline metal ion chelators, as describedin U.S. Pat. No. 5,648,270 to Kuhn et al. (1997).

Esters of the present invention are optionally prepared in chemicallyreactive forms and further conjugated to polymers such as dextrans toimprove their utility as sensors as described in U.S. Pat. Nos.5,405,975 and 5,453,517.

In another exemplary embodiment, the carrier molecule non-covalentlyassociates with organic or inorganic materials. Exemplary embodiments ofthe carrier molecule that possess a lipophilic substituent can be usedto target lipid assemblies such as biological membranes or liposomes bynon-covalent incorporation of the dye compound within the membrane,e.g., for use as probes for membrane structure or for incorporation inliposomes, lipoproteins, films, plastics, lipophilic microspheres orsimilar materials.

In an exemplary embodiment, the carrier molecule comprises a specificbinding pair member wherein the present compounds are conjugated to aspecific binding pair member and are used to detect an analyte in asample. Alternatively, the presence of the labeled specific binding pairmember indicates the location of the complementary member of thatspecific binding pair; each specific binding pair member having an areaon the surface or in a cavity which specifically binds to, and iscomplementary with, a particular spatial and polar organization of theother. Exemplary binding pairs are set forth in Table 2.

TABLE 2 Representative Specific Binding Pairs antigen antibody biotinavidin (or streptavidin or anti-biotin) IgG* protein A or protein G drugdrug receptor folate folate binding protein toxin toxin receptorcarbohydrate lectin or carbohydrate receptor peptide peptide receptorprotein protein receptor enzyme substrate enzyme DNA (RNA) cDNA (cRNA)†hormone hormone receptor ion chelator antibody antibody-binding proteins*IgG is an immunoglobulin †cDNA and cRNA are the complementary strandsused for hybridizationSolid Supports

In an exemplary embodiment, the compounds of the invention are bonded toa solid support, which includes semi-solid supports. A solid supportsuitable for use in the present invention is typically substantiallyinsoluble in liquid phases. Solid supports of the current invention arenot limited to a specific type of support. Rather, a large number ofsupports are available and are known to one of ordinary skill in theart. Thus, useful solid supports include semi-solids, such as aerogelsand hydrogels, resins, beads, biochips (including thin film coatedbiochips), multi-well plates (also referred to as microtitre plates),membranes, conducting and nonconducting metals and magnetic supports.More specific examples of useful solid supports include silica gels,polymeric membranes, particles, derivatized plastic films, glass beads,cotton, plastic beads, alumina gels, polysaccharides such as Sepharose,poly(acrylate), polystyrene, poly(acrylamide), polyol, agarose, agar,cellulose, dextran, starch, FICOLL, heparin, glycogen, amylopectin,mannan, inulin, nitrocellulose, diazocellulose, polyvinylchloride,polypropylene, polyethylene (including poly(ethylene glycol)), nylon,latex bead, magnetic bead, paramagnetic bead, superparamagnetic bead,starch and the like.

In some embodiments, the solid support may include a solid supportreactive functional group, including, but not limited to, hydroxyl,carboxyl, amino, thiol, aldehyde, halogen, nitro, cyano, amido, urea,carbonate, carbamate, isocyanate, sulfone, sulfonate, sulfonamide,sulfoxide, etc., for attaching the compounds of the invention. In apreferred embodiment, the solid supports contain a nucleophile (x), suchas amino, thiol, or hydroxyl.

A suitable solid phase support can be selected on the basis of desiredend use and suitability for various synthetic protocols. For example,where amide bond formation is desirable to attach the compounds of theinvention to the solid support, resins generally useful in peptidesynthesis may be employed, such as polystyrene (e.g., PAM-resin obtainedfrom Bachem Inc., Peninsula Laboratories, etc.), POLYHIPE™ resin(obtained from Aminotech, Canada), polyamide resin (obtained fromPeninsula Laboratories), polystyrene resin grafted with polyethyleneglycol (TentaGel™, Rapp Polymere, Tubingen, Germany),polydimethyl-acrylamide resin (available from Milligen/Biosearch,California), or PEGA beads (obtained from Polymer Laboratories).

Methods of Using the Present Labeling Reagents:

In one embodiment, the present invention provides methods of using thecompounds described herein to detect or monitor an analyte in a sampleor assay. In other embodiments, the compounds of the present inventionare utilized to label a sample or analyte to give a detectable ortraceable optical response under desired conditions by a) preparing alabeling solution comprising a compound of Formula I as described above,at a concentration sufficient to yield a detectable optical responseunder the desired conditions; combining the sample solution for a periodof time sufficient for the dye compound to yield a detectable responseunder the desired conditions; and c) detecting the optical response,preferably by illumination. Optionally, the sample is washed to removeresidual, excess or unbound label. The compound typically forms acovalent or non-covalent association or complex with an element of thesample, or is simply present within the bounds of the sample or portionof the sample.

In one embodiment, the compound of Formula I is used to determine aspecified characteristic of the sample by further comparing the opticalresponse with a standard or expected response. For example, the dyesolution is used to monitor specific components of the sample withrespect to their spatial and temporal distribution in the sample.

In a particular embodiment, wherein a solid support is labeled withlabeling reagent of present invention (such as a compound of FormulaIA), the reporter molecule is a ligand or receptor and the support formsa column, thereby forming an affinity column. In a preferred embodimentthe support is in a bead form. More particularly, the bead is a magneticbead.

For biological applications, the solution is typically an aqueous ormostly aqueous solution that comprises one or more of the describedcompounds. In one aspect of the invention, the solution comprises afluorophore as described above; alternatively, the dye solutioncomprises a hapten.

In an exemplary application of the present method, different features ofan analyte, e.g., a cell or epitopes of a molecule, are labeled withdifferent colored fluorescent conjugates. The target is detected and itsidentity is confirmed using the colocalization or “coincidence” of eachcolor on each target. Coincidence staining allows for the detection anddifferentiation of different organisms or strains of organismsexpressing different surface markers. Moreover, coincidence stainingprovides a method of distinguishing molecules of different structuredown to the level of isomeric differences and differences instereochemistry.

In the detection of pathogenesis, the most direct analyte is thepathogenic organism itself. In this case, assays preferably identifyparticular features of the organism such as surface proteins. To furtheraid in characterization, it is preferred to assay for molecular analytesas well. An example of a molecular analyte is an exotoxin such ascholera toxin. Antigen specific binding receptors are generated thatrecognize different characteristics of an analyte with high specificity.In the case of molecular analytes, receptors recognize differentepitopes of a protein or small molecule, while cellular analytes arerecognized through different molecules on the cell surface.

Although the fluorescence from each conjugate can be detectedsimultaneously, in one embodiment, to facilitate coincidence staining,the fluorescence from each analyte is detected independently.

In another exemplary embodiment, colocalization is used to differentiatebetween the formation of an analyte-conjugate complex and non-specificbinding of the analyte to another species within the assay system. Theintrinsic sensitivity of an assay often is limited by non-specificbinding of the analyte or other assay mixture components to thesubstrate. Single analyte coincidence staining can be used todifferentiate between specific binding of the analyte to the conjugateand non-specific binding of assay mixture components to the conjugatebased on the colocalization of fluorescent conjugate colors. Those ofskill in the art will appreciate that coincidence staining as describedherein is useful to distinguish non-specific binding in both solid-phase(e.g., gene chip) and solution-based assays

Coincidence staining can also be used to identify a single analyte. Forexample, one may wish to confirm the presence of a selected analyte in amixture of analytes that are structurally similar (e.g. having a commonepitope) or that have similar affinity for the component of theconjugate. In such circumstances, it may prove that the detection of asingle epitope is not sufficient for conclusive identification of atarget. Measuring the level of 2, preferably 3, more preferably 4 andeven more preferably 5 or more markers within a single analyte, providesan unambiguous profile specific for the analyte of interest.

In another exemplary embodiment, the present invention provides a methodfor distinguishing between organisms expressing the same surfacemarkers. Using coincidence staining, it is possible to identifydifferences in targets based on the ratio of surface marker expression.For example, despite intense efforts, no single binding-receptor hasbeen found for the unambiguous detection of B. anthracis spores, due toextensive cross-reactivity with related B. cereus and B. thuringiensis,which are genetically a single species (Helgason et al., Appl. Envir.Microbiol. 66:2627-2630 (2000)). Despite being of the same species,however, the relative amount of various surface proteins is differentbetween the three bacilli. Thus, multi-point detection of a variety ofmarkers at the single cell level will provide the specificity requiredto detect B. anthracis.

Diagnostic tests that detect the presence or absence of a single markerare unable to distinguish among strains that are nearly identical at thegenetic level, highlighting the need for new tools to distinguishbetween closely related organisms. Epidemics caused by emerging variantsof known pathogens are a common theme in infectious diseases (Jiang etal., Appl Environ Microbiol 66:148-53 (2000)) (Hedelberg et al. Nature406:477-483 (2000)). There is also the problem of deliberate engineeringof pathogens, incorporating virulence determinants from other species.An attack by such pathogens would be misdiagnosed due to the presence ofmarkers not normally found in the attacking pathogen. By probingmultiple markers within a single organism, using the methods of theinvention, such variants are detected and preferably identified.

In another exemplary embodiment the invention provides a method fordetecting a first analyte and a second analyte in a sample. The methodincludes incubating the sample with a composition of the invention thatincludes first and second fluorescent labeled conjugates. The componentof the first conjugate is a binding partner for the first analyte andthe component of the second conjugate is a binding partner for thesecond analyte. The incubation continues for a time and under conditionsappropriate to induce an interaction between at least a fraction of thepopulation of the first analyte with the first conjugate. During thisincubation period, it is generally preferred that a similar interactionoccurs between the second analyte and second conjugate, however, it iswithin the scope of the invention to change the incubation conditions asnecessary to drive the formation of a conjugate-analyte complex betweenthe second conjugate and second analyte.

Following the formation of at least the first analyte-conjugate complex,the sample is illuminated with light of a wavelength appropriate tocause the complex to fluoresce, thereby detecting the first analyte. Thesecond analyte is detected in a similar manner and may be detectedsimultaneously with the first analyte or by the sequential illuminationof the sample with wavelengths appropriate to induce the fluorescence ofeach fluorescent conjugate.

Solutions of the compounds of the invention are prepared according tomethods generally known in the art. As with related known fluorophoresand fluorogens, the dyes and dye-conjugates or reportermolecule-conjugates are generally soluble in water and aqueous solutionshaving a pH greater than or equal to about 6. The exact concentration ofreporter molecule-conjugate to be used is dependent upon theexperimental conditions and the desired results, and optimization ofexperimental conditions is typically required to determine the bestconcentration of stain to be used in a given application. Theconcentration of reporter molecule present in the solution typicallyranges from nanomolar to micromolar.

For those compounds of the present invention that are substituted bylipophilic moieties, the reporter molecule is optionally introduced intoliving cells by passive permeation through the cellular membranes. Lesscell-permeant compounds of the invention can be introduced into cells bypressure microinjection methods, scrape loading techniques (shortmechanical disruption of the plasma membrane where the plasma membraneis peeled away from the cytoplasm, the reporter molecule is perfusedthrough the sample and the plasma membrane is reassembled), patch clampmethods (where an opening is maintained in the plasma membrane for longperiods) or phagocytosis. Any other treatment that will permeabilize theplasma membrane, such as electroporation, shock treatments or highextracellular ATP can be used to introduce the reportermolecule-conjugate or blocked dye into the cellular cytoplasm.

In an exemplary embodiment of the invention, the reporter moleculesolution comprises a reporter molecule that non-covalently associateswith organic or inorganic materials. Exemplary embodiments of thereporter molecules that possess a lipophilic substituent can be used tostain lipid assemblies such as biological membranes or liposomes bynon-covalent incorporation of the dye compound within the membrane, e.g.for use as probes for membrane structure or for incorporation inliposomes, lipoproteins, films, plastics, lipophilic microspheres orsimilar materials.

The compounds of the invention can be used to reporter molecule cellsurfaces, cell membranes or intracellular compartments such asorganelles, or in the cell's cytoplasm. Certain reactive groups allowthe retention of the reporter molecules in cells or organelles byreacting with cellular materials. In particular, haloalkyl- orhalomethylbenzamide-substituted reagents are used to react selectivelywith intracellular components such as glutathione, or to retain the dyecompounds within cells or within selected organelles where the compoundis localized therein, according to methods previously described (U.S.Pat. No. 5,362,628 to Haugland et al, (1994); U.S. Pat. No. 5,576,424 toMao et al. (1996) (in cells); and U.S. Pat. No. 5,459,268 to Haugland etal. (1995) and U.S. Pat. No. 5,686,261 to Zhang et al. (1997) (inmitochondria); all incorporated by reference).Polyfluoroaryl-substituted dye compounds are similarly retained incells, in part by covalent attachment. The reactive reporter moleculesare used to localize staining in a part of the sample, e.g., where thelocalization of the corresponding functional group is indicative of acharacteristic of the sample; or to retain the dye in a specific portionof the sample for extended periods of time, e.g., to follow the stainedportion of the sample through a period of time or sequence of events.

In an exemplary embodiment the compound is a labeled member of aspecific binding pair, and is used as a fluorescent probe for thecomplementary member of that specific binding pair, each specificbinding pair member having an area on the surface or in a cavity whichspecifically binds to and is complementary with a particular spatial andpolar organization of the other. The fluorescent conjugate of a specificbinding pair member is useful for detecting and optionally quantifyingthe presence of the complementary specific binding pair member in asample, by methods that are well known in the art. Optionally, thecomplementary binding pair member is present in a animal cell, plantcell, bacteria, yeast or virus. Alternatively, the complementary memberis immobilized on a solid or semi-solid surface, such as a polymer,polymeric membrane or polymeric particle (such as a polymeric bead). Thedye-conjugate may also comprise a dye in a blocked form wherein theblock is later removed by the action of an enzyme or light.

Representative specific binding pairs (i.e. carrier molecules) are shownin Table 2. Typically a specific binding pair member or carrier moleculeconjugated to the reporter molecule (such as the compound of Formula I)is a ligand or a receptor. The term ligand means any organic compoundfor which a receptor naturally exists or can be prepared. A receptor isany compound or composition capable of recognizing a spatial or polarorganization of a molecule, e.g. epitopic or determinant site. Ligandsfor which naturally occurring receptors exist include natural andsynthetic proteins, including avidin and streptavidin, antibodies,enzymes, and hormones; nucleotides and natural or syntheticoligonucleotides, including primers for RNA and single- anddouble-stranded DNA; lipids; polysaccharides and carbohydrates; and avariety of drugs, including therapeutic drugs and drugs of abuse andpesticides. Methods extensively known in the art, to prepare antibodyconjugates for use in microscopy and immunofluorescent assays andnucleotide or oligonucleotide conjugates for nucleic acid hybridizationassays and nucleic acid sequencing are described in U.S. Pat. No.5,332,666 to Prober, et al. (1994); U.S. Pat. No. 5,171,534 to Smith, etal. (1992); U.S. Pat. No. 4,997,928 to Hobbs (1991); and WO Appl.94/05688 to Menchen, et al., and a wide variety of other applications.Nucleotide conjugates are readily incorporated by DNA polymerase and canbe used for in situ hybridization or other techniques.

In another preferred embodiment, the compounds of the invention areutilized as a component of one or more probes used in a multiplex assayfor detecting one or more species in a mixture. As used herein, the term“multiplex assay” refers to an assay in which fluorescence from two ormore dyes is detected, or in which fluorescence energy transfer betweentwo or more dyes and one or more quencher is detected.

Probes that include compounds of the invention are particularly usefulin performing multiplex-type analyses and assays. In a typical multiplexanalysis, two or more distinct species (or regions of one or morespecies) are detected using two or more probes, wherein each of theprobes is labeled with a different reporter molecule or fluorophore.Preferred species used in multiplex analyses generally meet at least twocriteria: the fluorescent species is bright and spectrally wellresolved; and the background fluorescence of the first dye does notsignificantly overlap the emission range of the second dye.

Thus, in a further embodiment, the invention provides a mixturecomprising at least a first and a second labeling reagent of theinvention. The first and second dyes are preferably conjugated to acomponent of a conjugate. The dyes may be conjugated to the samecomponent or to different components. In one preferred multiplexingassay, the dye is/are semiconductor nanocrystals.

Additionally, the present invention also provides a method for detectingor quantifying a particular molecular species. The method includes: (a)contacting the species with a mixture such as that described above; and(b) detecting a change in a fluorescent property of one or morecomponent of the mixture, the molecular species or a combinationthereof, thereby detecting or quantifying the molecular species.

The compounds of the invention are also of use in the numerousfluorescence polarization assays that use conjugates of fluorescent dyesto low molecular weight drugs and ligands, which will be improved by theuse of the dye compounds of the invention, e.g., U.S. Pat. Nos.4,420,568 to Wang (1983) and U.S. Pat. No. 4,510,251 to Kirkemo et al.(1985).

In those embodiments in which a reporter molecule is conjugated to aspecific binding pair member that is a chelator of calcium, sodium,magnesium, potassium, or other biologically important metal ion, theconjugate functions as an indicator of the ion, which indicators areoptionally further conjugated to a biological or plastic polymeraccording to methods known in the art; e.g., using analogs of thecompounds described in U.S. Pat. Nos. 5,453,517 to Kuhn, et al. (1995);U.S. Pat. No. 5,405,975 to Kuhn, et al. (1995).

In another exemplary embodiment, the compounds are substrates foroxidative enzymes and other reactive oxidizing agents, particularly forperoxidase enzymes. In another embodiment the compounds are used inkinase detection/inhibition assays, such as for the inhibition of Rafkinase, VEGF, CSF1R, GSK3, CHK1, CDK, PI3k, and the like.

In another exemplary embodiment, the compounds are used inpolynucleotide-based methods and assays. In a preferred embodiment, thelabeled carrier molecule is a polynucleotide which is used in gelelectrophoresis, PCR, cDNA libraries and the like. The probes formed byconjugating the reporter molecules to the polynucleotides as describedherein are particularly advantageous in their hydrolytic stability andconjugation reaction conditions which leave the polynucleotide strand intact. The probes can be used to screen for complementary nucleotidesequences in a sample.

The compounds also optionally contain additional substituents thatprovide additional advantages. For example, compounds modified tocontain a lipophilic tail according to the synthesis described in U.S.Pat. No. 5,208,148 to Haugland et al. (1993), are useful forpermeabilizing substrates for intracellular enzymes.

In another exemplary embodiment of the invention, the compounds are usedto determine the efficiency of a cellular efflux pump of cells in asample. Preferably the dye compounds are diacetates or diphosphates. Theefficiency of the cellular efflux pump of cells in the sample isdetermined by comparing the fluorescence emission of cells in the samplewith the fluorescence of cells having known efflux efficiency. Where theefflux pump is impaired, inhibited, or absent, the fluorescent compoundis well retained in the cell; where the efflux pump is present andfunctioning, the fluorescence of the cells decreases markedly. Thephotostability of the conjugate compounds is advantageous for monitoringthe time course of fluorescence.

Another application where the enhanced stability of the presentcompounds is particularly advantageous is use for tracing. One or morelabels conjugated to a biologically compatible polymer, including aminoacid polymers (typically proteins, including fluorescent proteins),carbohydrate polymers (typically dextrans), and polymeric microspheres(typically polystyrene) are readily prepared for use as tracersaccording to the method of the present invention.

The compounds of the invention are also of use in analytical methods,such as, to derivative low molecular weight compounds for their analysisby capillary zone electrophoresis (CZE), HPLC or other separationtechniques.

Sample Preparation:

The end user will determine the choice of the sample and the way inwhich the sample is prepared. The sample includes, without limitation,any material for labeling which contains a nucleophile amenable toreaction with the ester reagents of the present invention. Preferablythe material is biological derived or a synthetic macromolecule.

The sample can be a biological fluid such as whole blood, plasma, serum,nasal secretions, sputum, saliva, urine, sweat, transdermal exudates,cerebrospinal fluid, or the like. Biological fluids also include tissueand cell culture medium wherein an analyte of interest has been secretedinto the medium. Alternatively, the sample may be whole organs, tissueor cells from the animal. Examples of sources of such samples includemuscle, eye, skin, gonads, lymph nodes, heart, brain, lung, liver,kidney, spleen, thymus, pancreas, solid tumors, macrophages, mammaryglands, mesothelium, and the like. Cells include without limitationprokaryotic cells and eukaryotic cells that include primary cultures andimmortalized cell lines. Eukaryotic cells include without limitationovary cells, epithelial cells, circulating immune cells, β cells,hepatocytes, and neurons.

In many instances, it may be advantageous to add a small amount of anon-ionic detergent to the sample. Generally the detergent will bepresent in from about 0.01 to 0.1 vol. %. Illustrative non-ionicdetergents include the polyoxyalkylene diols, e.g. Pluronics, Tweens,Triton X-100, etc.

Illumination

The sample or medium in which the conjugate of the labeling reagent ofthe present invention is present is illuminated with a wavelength oflight selected to give a detectable optical response, and observed witha means for detecting the optical response. Equipment that is useful forilluminating the present compounds and compositions of the inventionincludes, but is not limited to, hand-held ultraviolet lamps, mercuryarc lamps, xenon lamps, lasers and laser diodes. These illuminationsources are optically integrated into laser scanners, fluorescencemicroplate readers or standard or microfluorometers.

The reporter molecules of the invention may, at any time after or duringan assay, be illuminated with a wavelength of light that results in adetectable optical response, and observed with a means for detecting theoptical response. Upon illumination, such as by an ultraviolet orvisible wavelength emission lamp, an arc lamp, a laser, or even sunlightor ordinary room light, the fluorescent compounds, including those boundto the complementary specific binding pair member, display intensevisible absorption as well as fluorescence emission. Selected equipmentthat is useful for illuminating the fluorescent compounds of theinvention includes, but is not limited to, hand-held ultraviolet lamps,mercury arc lamps, xenon lamps, argon lasers, laser diodes, and YAGlasers. These illumination sources are optionally integrated into laserscanners, fluorescence microplate readers, standard or minifluorometers, or chromatographic detectors. This fluorescence emissionis optionally detected by visual inspection, or by use of any of thefollowing devices: CCD cameras, video cameras, photographic film, laserscanning devices, fluorometers, photodiodes, quantum counters,epifluorescence microscopes, scanning microscopes, flow cytometers,fluorescence microplate readers, or by means for amplifying the signalsuch as photomultiplier tubes. Where the sample is examined using a flowcytometer, a fluorescence microscope or a fluorometer, the instrument isoptionally used to distinguish and discriminate between the fluorescentcompounds of the invention and a second fluorophore with detectablydifferent optical properties, typically by distinguishing thefluorescence response of the fluorescent compounds of the invention fromthat of the second fluorophore. Where a sample is examined using a flowcytometer, examination of the sample optionally includes isolation ofparticles within the sample based on the fluorescence response by usinga sorting device. In another embodiment, the illumination source is usedto form a covalent bond between the present dye and an analyte ofinterest. In this instance the dye comprises a photoactivatable reactivegroup, such as those discussed above.

Kits

Additional embodiments of the present invention include kits comprisingthe labeling reagents described herein for use in labeling carriermolecules or solid supports. In addition to the compounds, the kitsinclude instructions on how to reporter molecule the carrier molecule orsolid support. One particular embodiment provides a kit for forming aconjugate with a carrier molecule or solid support and a labelingreagent, wherein the kit comprises:

-   -   a) a labeling reagent according to Formula IA or a tautomer or        salt thereof:

-   -   wherein,    -   L is a linker;    -   R¹ is a halogen;    -   R² is a halogen;    -   R³ comprises a water solubilizing group; and    -   R^(a) is a reporter molecule;    -   b) instructions for forming a conjugate with the carrier        molecule or solids support.

Various ancillary materials will frequently be employed in an assay inaccordance with the present invention. In an exemplary embodiment,buffers and/or stabilizers are present in the kit components. In anotherexemplary embodiment, the kits comprise indicator solutions or indicator“dipsticks”, blotters, culture media, cuvettes, and the like. In yetanother exemplary embodiment, the kits comprise indicator cartridges(where a kit component is bound to a solid support) for use in anautomated detector. In another exemplary embodiment, the kit furthercomprises molecular weight markers, wherein said markers are selectedfrom phosphorylated and non-phosphorylated polypeptides, calcium-bindingand non-calcium binding polypeptides, sulfonated and non-sulfonatedpolypeptides, and sialylated and non-sialylated polypeptides. In anotherexemplary embodiment, the kit further comprises a member selected from afixing solution, a detection reagent, a standard, a wash solution, andcombinations thereof.

A detailed description of the invention having been provided above, thefollowing examples are given for the purpose of illustrating theinvention and shall not be construed as being a limitation on the scopeof the invention or claims.

EXAMPLES Example 1 BODIPY ester of 2,6-difluoroactivated phenol,solubilized with sulfo group (compound 4)

4-((3,5-difluoro-4-hydroxyphenyl)diazenyl)benzenesulfonic acid (2)

Sulfanilic acid (0.767 g, 4.43 mmol) was dissolved in hot mixture of 20mL of water and 10 mL of conc. HCl. The solution was cooled in ice/NaClbath to 0° C. giving a suspension of HCl salt. The solution of sodiumnitrite (0.367 g, 5.32 mmol in 5 mL of water) was added dropwise to thesuspension of ammonium salt, maintaining the temperature below +5° C.All solid dissolved and the resulting solution was stirred for 20 min.After that white precipitate formed again and the resulting suspensionwas added dropwise to the mixture of 2,6-difluorophenol (0.576 g, 4.43mmol) in 10 mL of dioxane and KOH (10 g) in 15 mL of water, cooled inice/water bath. The reaction mixture was stirred for 30 min in ice/waterbath and then extracted with ethyl acetate (3×30 mL). The aqueoussolution was acidified with 10% HCl to pH 2-3 and the formed yellowprecipitate was collected, washed with water and dried in vacuum to givephenol 2 as a yellow powder (1.1 g, 79%).

3-(3-(2,6-Difluoro-4-((4-sulfophenyl)diazenyl)phenoxy)-3-oxopropyl)-5,5-difluoro-7,9-dimethyl-5H-dipyrrolo[1,2-c:1′,2′-f][1,3,2]diazaborinin-4-ium-5-uide(4)

Acid 3 (0.019 g, 0.065 mmol) and phenol 2 (0.020 g, 0.064 mmol) weredissolved in 2 mL of dry DMF. EDC (0.015 g, 0.078 mmol) was added to thesolution and the reaction mixture was stirred overnight at rt. Then itwas concentrated in vacuum and the crude product was purified by columnchromatography on silica gel using 60:10:1 chloroform-methanol-aceticacid as an eluant to give ester 4 as an orange powder (0.015 g, 39%).

Example 2 BODIPY ester of 2,6-dichloro activated phenol, solubilizedwith two carboxylic groups (compound 8)

2-((3,5-Dichloro-4-hydroxyphenyl)diazenyl)terephthalic acid (6)

2-Aminoterephtalic acid (0.500 g, 2.76 mmol) was dissolved in hotmixture of 30 mL of water and 10 mL of conc. HCl. The solution wascooled in ice/NaCl bath to 0° C. giving a suspension of HCl salt. Thesolution of sodium nitrite (0.230 g, 3.33 mmol in 10 mL of water) wasadded dropwise to the suspension of ammonium salt, maintaining thetemperature below +5° C. The resulting solution was stirred for 20 minand added dropwise to the solution of 2,6-dichlorophenol (0.450 g, 2.76mmol) in 80 mL of 2M KOH, cooled in ice/water bath. The reaction mixturewas stirred for 2 hrs in ice/water bath and then acidified with 10% HClto pH 2-3 and extracted with ethyl acetate (3×30 mL). The combinedextract was washed with brine (30 mL), dried over Na₂SO₄ and evaporated.The crude product was purified by column chromatography on silica gelusing 60:15:1 chloroform-methanol-acetic acid as an eluant to givephenol 6 as a orange solid (0.200 g, 20%).

3-(3-(2,6-Dichloro-4-((2,5-dicarboxyphenyl)diazenyl)phenoxy)-3-oxopropyl)-5,5-difluoro-7,9-dimethyl-5H-dipyrrolo[1,2-c:1′,2′-f][1,3,2]diazaborinin-4-ium-5-uide(8)

3-(2-Carboxyethyl)-5,5-difluoro-7,9-dimethyl-5H-dipyrrolo[1,2-c:1′,2′-f][1,3,2]diazaborinin-4-ium-5-uide (3, 0.013 g, 0.044 mmol) wasdissolved in 5 mL of dry methylene chloride. The solution was cooled inice/water bath and then oxalyl chloride (0.02 mL, 0.2 mmol) was added tothe solution followed by adding of one drop of DMF as a catalyst. After15 min the reaction mixture was evaporated in vacuum and the residue wasre-evaporated from toluene. The resulting acyl chloride 7 was dissolvedin 5 mL of dry methylene chloride and added to the solution of phenol 6(0.016 g, 0.045 mmol) in 3 mL of DMF, containing DIEA (0.039 mL, 0.22mmol). The reaction mixture was stirred for 30 min at RT and thendiluted with 10% HCl (50 mL). The product was extracted with ethylacetate (2×20 mL). The combined extract was washed with brine (30 mL),dried over Na₂SO₄ and evaporated. The crude product was purified bycolumn chromatography using 100:10:0.5 chloroform-methanol-acetic acidas an eluant to give phenol ester 8 (0.010 g, 36%) as an orange solid.

Example 3 BODIPY ester of 2,6-difluoro activated phenol, solubilizedwith two carboxylic groups (compound 10)

2-((3,5-Difluoro-4-hydroxyphenyl)diazenyl)terephthalic acid (9)

2-Aminoterephtalic acid (1.00 g, 5.52 mmol) was dissolved in hot mixtureof 60 mL of water and 20 mL of conc. HCl. The solution was cooled inice/NaCl bath to 0° C. giving a suspension of HCl salt. The solution ofsodium nitrite (0.460 g, 6.67 mmol in 10 mL of water) was added dropwiseto the suspension of ammonium salt, maintaining the temperature below+5° C. The resulting solution was stirred for 20 min and then addeddropwise to the solution of 2,6-difluorophenol (0.720 g, 5.53 mmol) in50 mL of 1 M KOH, cooled in ice/water bath. The reaction mixture wasstirred for 1.5 hrs in ice/water bath and then acidified with 10% HCl topH 2-3. The resulting precipitate was collected, washed with water anddried in vacuum to give phenol 9 as an orange solid (0.5 g, 28%).

3-(3-(2,6-Difluoro-4-((2,5-dicarboxyphenyl)diazenyl)phenoxy)-3-oxopropyl)-5,5-difluoro-7,9-dimethyl-5H-dipyrrolo[1,2-c:1′,2′-f][1,3,2]diazaborinin-4-ium-5-uide(10)

3-(2-Carboxyethyl)-5,5-difluoro-7,9-dimethyl-5H-dipyrrolo[1,2-c:1′,2′-f][1,3,2]diazaborinin-4-ium-5-uide (3, 0.020 g, 0.068 mmol) wasdissolved in 5 mL of dry methylene chloride. The solution was cooled inice/water bath and then oxalyl chloride (0.03 mL, 0.34 mmol) was addedto the solution followed by adding one drop of DMF as a catalyst. After15 min the reaction mixture was evaporated in vacuum and the residue wasre-evaporated from toluene. The resulting acyl chloride 7 was dissolvedin 5 mL of dry methylene chloride and added to the solution of phenol 9(0.022 g, 0.068 mmol) in 3 mL of DMF, containing DIEA (0.060 mL, 0.34mmol). The reaction mixture was stirred for 30 min at RT and thendiluted with 50 mL of ethyl acetate. The mixture was washed with 10% HCl(3×20 mL), brine (30 mL), dried over Na₂SO₄ and evaporated. The crudeproduct was purified by column chromatography using 100:10:0.5chloroform-methanol-acetic acid as an eluant to give phenol ester 10(0.020 g, 49%) as an orange solid.

Example 4 BODIPY ester of 2,6-difluoro activated phenol, solubilizedwith triethyleneglycol substituent (compound 20)

2-(2-(2-methoxyethoxy)ethoxy)ethyl 4-methyl benzenesulfonate (15)

Triethylene glycol monomethyl ether (14, 2.00 mL, 12.8 mmol) wasdissolved in 5 mL of pyridine and the solution was cooled in ice/waterbath. Tosyl chloride was added portionwise to the solution of 14 and thereaction mixture was stirred for 30 min in ice/water bath. The n it wasdiluted with 100 mL of toluene and evaporated. The residue was mixedwith 30 mL of 10% HCl and the product was extracted with ethyl acetate(3×30 mL). The combined extract was washed with water (30 mL), brine (30mL), dried over Na₂SO₄ and evaporated to give tosylate 15 as a clear oil(3.50, 86%).

1-(2-(2-(2-methoxyethoxy)ethoxy)ethoxy)-4-nitrobenzene (16)

Tosylate 15 (1.14 g, 3.58 mmol) and p-nitrophenol (0.50 g, 3.6 mmol)were dissolved in 20 mL of acetonitrile. Powdered K₂CO₃ (0.50 g, 3.6mmol) was added to the solution and the mixture was stirred overnightunder reflux. Then the mixture was cooled to rt and diluted with 50 mLof water. The product was extracted with ethyl acetate (3×30 mL). Thecombined extract was washed with water (2×30 mL), brine (30 mL), driedwith Na₂SO₄ and evaporated to give 16 (0.94 g, 90%) as a clear oil.

4-(2-(2-(2-methoxyethoxy)ethoxy)ethoxy)aniline (17)

Nitro compound 17 (1.01 g, 3.54 mmol) was dissolved in 30 mL ofmethylene chloride. 10% Palladium on carbon (100 mg) was added and thereaction mixture was shaken at 40 psi of hydrogen in Parr apparatus for2 hrs. The reaction mixture was filtered from the catalyst andevaporated. The crude product was purified by chromatography on silicagel column using 2:1 ethyl acetate-chloroform mixture as an eluant togive aniline 17 as a dark oil (0.436 g, 48%).

2,6-difluoro-4-((4-(2-(2-(2-methoxyethoxy)ethoxy)ethoxy)phenyl)diazenyl)phenol(18)

4-(2-(2-(2-methoxyethoxy)ethoxy)ethoxy)aniline (17) (0.436 g, 1.71 mmol)was dissolved in hot mixture of 20 mL of water and 0.5 mL of conc. HCl.The solution was cooled in ice/NaCl bath to 0° C. and then the solutionof sodium nitrite (0.140 g, 2.03 mmol in 4 mL of water) was addeddropwise to the solution of ammonium salt, maintaining the temperaturebelow +5° C. The resulting solution of diazonium salt was stirred for 30min and then added dropwise to the solution of 2,6-difluorophenol (0.220g, 1.69 mmol) in 10 mL of 1 M KOH, cooled in ice/water bath. Thereaction mixture was stirred for 40 min in ice/water bath and thenacidified with 10% HCl to pH 2-3 and extracted with ethyl acetate (4×40mL). The combined extract was washed with brine (30 mL), dried overNa₂SO₄ and evaporated. The crude product was purified by columnchromatography on silica gel using 2:1 chloroform-ethyl acetate mixtureas an eluant to give phenol 18 as a orange solid (0.094 g, 14%).

7-(2-carboxyethyl)-3-(3-(2,6-difluoro-4-((4-(2-(2-(2-methoxyethoxy)ethoxy)ethoxy)phenyl)diazenyl)phenoxy)-3-oxopropyl)-5,5-difluoro-5H-dipyrrolo[1,2-c:1′,2′-f][1,3,2]diazaborinin-4-ium-5-uide(20)

3,7-Bis(2-carboxyethyl)-5,5-difluoro-5H-dipyrrolo[1,2-c:1′,2′-f][1,3,2]diazaborinin-4-ium-5-uide (19, 0.035 g, 0.11 mmol) andphenol 18 (0.046 g, 0.12 mmol) were dissolved in the mixture of 1 mL ofDMF and 1 mL of acetinitrile. EDC (0.022 g, 0.12 mmol) was added tosolution and the reaction mixture was stirred overnight at rt and thenevaporated in vacuum. The crude product was purified by columnchromatography on silica gel using 100:100:0.5 chloroform-ethylacetate-acetic acid mixture to give ester 20 as an orange solid (0.040g, 51%).

Example 5

To a 1 M solution of potassium hydroxide (20.8 ml, 0.0208 mol) was added3,5-dichloro-4-hydroxybenzenesulfonic acid (97) (2.553 g, 0.0105 mol)and the purple solution was stirred at room temperature for 1 hour. Thereaction mixture was filtered through a pipette containing a glass woolplug to remove any remaining brown solids. The filtrate was frozen ondry ice and lyophilized to give 3.04 g (91% yield) of 98 as a lightpurple solid.

Example 6

To a suspension of 98 (300 mg, 0.942 mmol) in anhydrous acetonitrile wasadded 99 (264 mg, 0.942 mmol), and the suspension was stirred underargon at room temperature for 18 hours. The reaction mixture wascentrifuged to remove the precipitate and the supernatant was decantedand evaporated in vacuo. Fresh acetonitrile (3 ml) was added and theresulting solution added dropwise to a stirred solution of ether (60 ml)to give a white precipitate. The precipitate was allowed to settle andthe ether decanted. Fresh ether (60 ml) was added, stirred, allowed tosettle, and decanted two more times. The resulting white precipitate wasdried under high vacuum to give 338 mg (70% yield) of 101 as a whitepowder.

Example 7

To a mixture of compound 100 (350 mg, 0.418 mmol) and DMAP (51 mg, 0.418mmol) in anhydrous DMF (35 ml) was added 4-oxa-(potassium3,5-dichloro-4-oxidobenzenesulfonate) tetramethyluroniumhexafluorophosphate (101) (255 mg, 0.501 mmol) to give an orangesuspension that was stirred at room temperature under argon for 24 hrs.The reaction mixture was added dropwise to stirring ethyl acetate (350ml). The mixture was centrifuged and the supernatant removed. Additionalethyl acetate (300 ml) was added and the precipitate resuspended, thencentrifuged and the supernatant removed. This was repeated 2 more times.Acetonitrile (300 ml) was then added and the precipitate resuspended,then centrifuged and the supernatant removed. Purification by silica gelchromatography (acetonitrile:water, 98:2 to 92:8) afforded 217 mg (63%yield) of 102 as a dark orange solid.

Example 8

To a mixture of Compound 103 (50 mg, 0.0597 mmol) and DMAP (1 mg) inanhydrous DMF (5 ml) was added 4-oxa-(potassium3,5-dichloro-4-oxidobenzenesulfonate) tetramethyluroniumhexafluorophosphate (101) (60 mg, 0.119 mmol) to give an orangesuspension that was stirred at room temperature under argon for 6 days.The reaction mixture was added dropwise to stirring ethyl acetate (30ml). The mixture was centrifuged and the supernatant removed. Additionalethyl acetate (30 ml) was added and the precipitate resuspended, thencentrifuged and the supernatant removed. Purification by silica gelchromatography (acetonitrile:water, 95:5 to 90:10) afforded 10 mg (15%yield) of 104 as a dark orange solid.

Example 9

To a mixture of amino-dPEG₄-acid (106) (14 mg, 0.054 mmol) and 1 Mtriethylammonium bicarbonate (0.18 ml, 0.18 mmol) in water (0.5 ml) wasadded Compound 105 (30 mg, 0.036 mmol) and the reaction was stirred atroom temperature for 2 hours. The solvent was evaporated in vacuo, water(2 ml) added and evaporated, and this was repeated twice more.Purification by LH-20 column (eluent: water) afforded 15 mg (41% yield)of 107 as an orange solid.

To a mixture of 107 (12 mg, 0.012 mmol) and DMAP (1 mg) in anhydrous DMF(1 ml) was added 4-oxa-(potassium 3,5-dichloro-4-oxidobenzenesulfonate)tetramethyluronium hexafluorophosphate (101) (14 mg, 0.026 mmol). Thereaction mixture was stirred for 3 hours at room temperature underargon, and the solvent was removed in vacuo. Acetonitrile (3 ml) wasadded and the suspension was sonnicated and stirred, then centrifugedand the supernatant removed. This was repeated 3 times. Purification bysilica gel chromatography (acetonitrile:water, 8:2) afforded 108 as anorange solid.

Example 10

To a mixture of isonipecotic acid (7 mg, 0.054 mmol) and 1 Mtriethylammonium bicarbonate (0.18 ml, 0.18 mmol) in water (0.5 ml) wasadded Compound 105 (30 mg, 0.036 mmol) and the reaction was stirred atroom temperature for 24 hours. The solvent was evaporated in vacuo,water (2 ml) added and evaporated, and this was repeated twice more.Purification by LH-20 column (eluent: water) afforded 13 mg (43% yield)of 109 as an orange solid.

To a mixture of 109 (17 mg, 0.020 mmol) and DMAP (1 mg) in anhydrous DMF(1 ml) was added 4-oxa-(potassium 3,5-dichloro-4-oxidobenzenesulfonate)tetramethyluronium hexafluorophosphate (101) (11 mg, 0.022 mmol). Thereaction mixture was stirred for 2 hours at room temperature underargon, and the solvent was removed in vacuo. Acetonitrile (3 ml) wasadded and the suspension was sonnicated and stirred, then centrifugedand the supernatant removed. This was repeated 3 times. Residual solventwas removed in vacuo to provide 110 as an orange solid.

Example 11

To a mixture of 109 (7 mg, 0.0079 mmol) and DMAP (1 mg) in anhydrous DMF(1 ml) was added O-(1,3-dichloro-2-oxidobenzene) tetramethyluroniumhexafluorophosphate (111) (8 mg, 0.019 mmol). The reaction mixture wasstirred for 24 hours at room temperature under argon, and the solventwas removed in vacuo. Purification by silica gel chromatography(acetonitrile:water, 8:2) afforded 3 mg (38% yield) of 112 as an orangesolid.

Example 12

To a mixture of Compound 113 (100 mg, 0.086 mmol), DMAP (10.5 mg, 0.086mmol) and triethylamine (27 mg, 0.267 mmol) in anhydrous DMF (10 ml) wasadded 4-oxa-(potassium 3,5-dichloro-4-oxidobenzenesulfonate)tetramethyluronium hexafluorophosphate (101) (53 mg, 0.103 mmol) to givea blue solution that was stirred at room temperature under argon for 24hrs. The reaction mixture was added dropwise to stirring ethyl acetate(100 ml). The mixture was centrifuged and the supernatant removed.Additional ethyl acetate (100 ml) was added and the precipitateresuspended, then centrifuged and the supernatant removed. This wasrepeated 2 more times. Acetone (100 ml) was then added and theprecipitate resuspended, then centrifuged and the supernatant removed.Removal of excess solvent in vacuo provided 82 mg (65% yield) of 114 asa blue solid.

Example 13

Combine Compound 122 (0.10 mmol), DMAP (0.10 mmol), and triethylamine(0.14 mmol) in anhydrous DMF (10 ml). Add 4-oxa-(potassium3,5-dichloro-4-oxidobenzenesulfonate) tetramethyluroniumhexafluorophosphate (101) (0.11 mmol) and stir the reaction mixture atroom temperature under argon for 24 hrs. Add the reaction mixturedropwise to stirring ethyl acetate to precipitate the product andcentrifuge the suspension to isolate the product. Purify by silica gelcolumn chromatography using acetonitrile/water as the eluent to afford123 as a red solid.

Example 14

Combine Compound 124 (0.10 mmol), DMAP (0.10 mmol), and triethylamine(0.29 mmol) in anhydrous DMF (10 ml). Add 4-oxa-(potassium3,5-dichloro-4-oxidobenzenesulfonate) tetramethyluroniumhexafluorophosphate (101) (0.13 mmol) and stir the reaction mixture atroom temperature under argon for 24 hrs. Add the reaction mixturedropwise to stirring ethyl acetate to precipitate the product andcentrifuge the suspension to isolate the product. Purify by silica gelcolumn chromatography using acetonitrile/water as the eluent to afford125 as a purple solid.

Example 15

Combine Compound 126 (0.10 mmol) and DMAP (0.10 mmol) in anhydrous DMF(10 ml). Add 4-oxa-(potassium 3,5-dichloro-4-oxidobenzenesulfonate)tetramethyluronium hexafluorophosphate (101) (0.30 mmol) and stir thereaction mixture at room temperature under argon for 24 hrs. Add thereaction mixture dropwise to stirring ethyl acetate to precipitate theproduct and centrifuge the suspension to isolate 127 as a blue solid.

Example 16

Combine BODIPY FL carboxylic acid (128) (0.10 mmol), DMAP (0.10 mmol)and anhydrous pyridine (0.20 mmol) in anhydrous DMF (10 ml). Add4-oxa-(potassium 3,5-dichloro-4-oxidobenzenesulfonate)tetramethyluronium hexafluorophosphate (101) (0.20 mmol) and stir thereaction mixture at room temperature under argon for 24 hrs. Add thereaction mixture dropwise to stirring ethyl acetate to precipitate theproduct and centrifuge the suspension to isolate 129 as an orange solid.

Example 17

Combine Compound 130 (0.10 mmol), DMAP (0.10 mmol), and triethylamine(0.20 mmol) in anhydrous DMF (10 ml). Add 4-oxa-(potassium3,5-dichloro-4-oxidobenzenesulfonate) tetramethyluroniumhexafluorophosphate (101) (0.20 mmol) and stir the reaction mixture atroom temperature under argon for 24 hrs. Add the reaction mixturedropwise to stirring ethyl acetate to precipitate the product. Decantthe ethyl acetate and add 4 M HCl in dioxane with stirring. Centrifugethe suspension to collect the precipitate and isolate 131 as a lightyellow solid.

Example 18

Combine Oregon Green carboxylic acid (132) (0.10 mmol), DMAP (0.10 mmol)and anhydrous pyridine (0.20 mmol) in anhydrous DMF (10 ml). Add4-oxa-(potassium 3,5-dichloro-4-oxidobenzenesulfonate)tetramethyluronium hexafluorophosphate (101) (0.12 mmol) and stir thereaction mixture at room temperature under argon for 24 hrs. Add thereaction mixture dropwise to stirring ethyl acetate to precipitate theproduct and centrifuge the suspension to isolate 133 as a yellow solid.

Example 19

Combine Cy3 carboxylic acid (134) (0.10 mmol), DMAP (0.10 mmol), andtriethylamine (0.31 mmol) in anhydrous DMF (10 ml). Add 4-oxa-(potassium3,5-dichloro-4-oxidobenzenesulfonate) tetramethyluroniumhexafluorophosphate (101) (0.12 mmol) and stir the reaction mixture atroom temperature under argon for 24 hrs. Add the reaction mixturedropwise to stirring ethyl acetate to precipitate the product andcentrifuge the suspension to isolate 135 as a purple solid.

Example 20

Combine biotin (136) (0.10 mmol), DMAP (0.10 mmol) and anhydrouspyridine (0.25 mmol) in anhydrous DMF (10 ml). Add 4-oxa-(potassium3,5-dichloro-4-oxidobenzenesulfonate) tetramethyluroniumhexafluorophosphate (101) (0.16 mmol) and stir the reaction mixture atroom temperature under argon for 24 hrs. Add the reaction mixturedropwise to stirring ethyl acetate to precipitate the product andcentrifuge the suspension to isolate 133 as a colorless solid.

-   -   Compound 120 Reporter molecule TFP

-   -   Compound 121: Reporter molecule SE

-   -   Compound 122: Labeled DCP

Results:

Samples were incubated at room temperature in the indicated solution.Aliquots were taken at 1, 2, 3, 4 and 24 hrs and analyzed by HPLC todetermine percent hydrolysis, from which the average half-life wasdetermined.

TABLE 1 Hydrolysis Half-Life Data E-pure H₂O 25 mM phosphate Compound pH~5 DMSO buffer pH 8.6 Compound 102 21 days 16 days 28 hrs Compound 104 —— 17 hrs Compound 105 — — 74 min Compound 120 — — 78 min Compound 108 —— 6 hrs Compound 110 — — 1.5 hrs Compound 112 — — 122 hrs Compound 122 —— 16 hrs Compound 114 — — 102 min Compound 121 — — 105 min

Samples were incubated at room temperature in the indicated solution.Aliquots were taken at 1, 2, 3, 4 and 24 hrs and analyzed by HPLC todetermine percent hydrolysis, from which the average half-life wasdetermined. Results are shown in Table 2.

TABLE 2 Hydrolysis Half-Life Data in Various Buffer Solutions Compound102 Compound 105 Compound 120 25 mM phosphate 28 hrs 74 min 78 minbuffer pH 8.6 10 mM HEPES 159 hrs 4 hrs 6.5 hrs buffer pH 8.2, 0.2M NaCl20 mM Tris buffer 77 hrs 12 min 139 min pH 8.6 25 mM Borate 3.5 hrs <5min <5 min buffer pH 8.6 25 mM phosphate 245 hrs 111 min 173 min bufferpH 7.2 20 mM Tris buffer 1019 hrs 244 min 836 min pH 7 25 mM phosphate38 min <2 min <2 min buffer pH 8.6 w/10 mM imidazole 20 mM Tris buffer95 min <1 min <1 min pH 8.6 w/50 mM NaN₃

Samples were incubated with Compound 102 at room temperature for 1 hourin the designated buffer. Antibody labeling occurs in each buffersystem. Results are shown in Table 3.

TABLE 3 Goat anti-Mouse Antibody Degree of Labeling with Compound 102Molar Molar Molar Molar Ratio 5 Ratio 10 Ratio 15 Ratio 20 25 mM 4.5 7.510.0 12.6 phosphate buffer pH 8.6 10 mM HEPES 2.1 3.2 4.8 5.0 buffer pH8.2, 0.2M NaCl 20 mM Tris 2.2 3.0 3.5 3.8 buffer pH 8.6

Samples were incubated with Compound 102 at a molar ratio of 12 in thedesignated buffer at room temperature for the specified incubation time.Higher degrees of labeling are possible with longer incubation times,depending on the buffer system. Results are shown in Table 4.

TABLE 4 Degree of Antibody Labeling at Long Incubation Times withCompound 102 Degree of Labeling Incubation Time 25 mM phosphate bufferpH 8.9  3 hrs 8.6 25 mM phosphate buffer pH 6.5  6 hrs 7.2 10 mM HEPESbuffer pH 8.6 20 hrs 8.2, 0.2M NaCl 20 mM Tris buffer pH 8.6 7.5 12 hrs

2-(6-amino-3-iminio-4,5-disulfonato-3H-xanthen-9-yl)benzoate, comprisingan SDP ester was prepared and compared to commercially available2-(6-amino-3-iminio-4,5-disulfonato-3H-xanthen-9-yl)benzoate comprisinga succinimidyl ester (SE) and2-(6-amino-3-iminio-4,5-disulfonato-3H-xanthen-9-yl)benzoate comprisinga TFP for hydrolytic stability in 25 mM Pi buffer pH 8.6. The SEcompound had a half-life of 74 min and TFP had a half-life of 78 min,while the SDP had a half-life of 28 hours. This dramatic increase inhydrolytic stability has significant impact on the preparation andpurification, ease of handling, storage stability, and biomoleculelabeling efficiency. After preparation of the SDP, the crude compoundwas purified to 98% purity by silica gel flash chromatography usingacetonitrile/water as the eluent. Purification is not possible with SE(prepared and sold in 50-70% purity) or TFP (prepared and sold in 50-80%purity) because of their hydrolytic instability. The SDP is also stableto lyophylization which greatly increases the ease of handling andpackaging. With greater hydrolytic stability also comes less degradationupon storage than Compound 120 and Compound 105. In addition, with morehydrolytic stability comes greater labeling efficiency, with AF488 SDPgiving nearly twice as much biomolecule labeling as an equivalent amountof Compound 105.

Each of the above-cited references are hereby incorporated by referenceas if set forth fully herein.

The invention claimed is:
 1. A compound having the following structureor a tautomer or salt thereof:

wherein, R¹ is a halogen; R² is a halogen; and R³ is a watersolubilizing group.
 2. The compound of claim 1, wherein R¹ and R² arechloro.
 3. The compound of claim 1, wherein R³ is —SO₃ ^(′.)
 4. Thecompound of claim 1, wherein R¹ and R² are chloro and wherein R³ is —SO₃^(−.)
 5. The compound of claim 1 wherein the water solubilizing groupcomprises a polar substituent.
 6. The compound of claim 1 wherein thewater solubilizing group comprises a charged substituent that increaseswater solubility of a base molecule.
 7. The compound of claim 6 whereinthe water solubilizing group comprises an anionic substituent.
 8. Thecompound of claim 6 wherein the water solubilizing group is appendeddirectly to the base molecule.
 9. The compound of claim 6 wherein thewater solubilizing group is appended through a linker to the basemolecule.
 10. The compound of claim 1 wherein the water solubilizinggroup comprises a carboxyl group, sulphonic acid, hydroxyl group,substituted azenyl group, a polyoxyalkylene, phosphate group, or abisphosphonate group.
 11. The compound of claim 10 wherein the watersolubilizing group comprises a polyoxyalkylene and the polyoxyalkyleneis poly (ethylene glycol).
 12. The compound of claim 1 wherein the watersolubilizing group comprises a substituent that introduces an additionalnet charge into the molecule.